Optimizing Shrimp Culture Through Environmental Monitoring: Effects of Water Quality and Metal Ion Profile on Whiteleg Shrimp (Litopenaeus vannamei) Performance in a Semi-Intensive Culture Pond

Abstract

Water quality management is crucial for sustainable whiteleg shrimp (Litopenaeus vannamei) aquaculture, though little research has comprehensively investigated the spatiotemporal fluctuation of trace elements in tropical semi-intensive ponds. This study investigated the water quality variations and trace element concentrations in an earthen pond across a 56-day culture cycle during the dry season. Physicochemical parameters (temperature, pH, salinity, dissolved oxygen, ammonia, nitrite, and nitrate) and trace elements (Cu, Zn, Mn, Fe, and Mg) were measured concurrently with shrimp growth and survival. The DO and pH readings were observed to fluctuate significantly during the mid-to-late stages of culture, with DO nearing critical thresholds (<5.0 mg L⁻¹). A sudden increase in ammonia and nitrite levels suggested the accumulation of organic matter and a microbial imbalance. Zinc concentrations (0.28–1.00 mg L⁻¹) approached stress-inducing levels, while magnesium remained low (10.44–10.72 mg L⁻¹). Pearson’s correlation revealed strong positive associations between ammonia and nitrate (r = 0.95) and between DO and pH (r = 0.94), while Mg was negatively correlated with Fe (r = −0.99) and nitrite (r = −0.88). Shrimp achieved 13.43 ± 0.73 g mean weight, with 77.8% survival and an FCR of 1.08. These results provide baseline evidence that combined water quality and trace element monitoring can become an early warning framework for pond management. Future studies integrating shrimp physiology and immune responses are needed to establish direct causal relationships.

1. Introduction

Shrimp farming is one of the important parts of Malaysia’s agri-food sector, which contributes to the local food supply and export income [1]. Due to Malaysia’s warm weather and long coastline, it becomes a great place for shrimp farming, specifically Litopenaeus vannamei, a species commonly farmed in Southeast Asia, including Thailand and Vietnam. This shrimp is popular because it can adapt well to various environments and has good taste and texture [2,3]. Malaysia has produced approximately 47,000 metric tonnes of shrimp every year, and Litopenaeus vannamei is the main species for culture production. This species has a high demand in local and international markets and at times was able to adapt to intensive system culture [1,4]. However, the dynamic of pond ecosystems and fluctuations of water and trace elements still become the problems to overcome because of the impacts on shrimp health, growth, survival, disease outbreaks, and feed efficiency [4,5]. Crucial water quality parameters relate to the survival of shrimp and their growth, as when these levels become too high, shrimp will be easily exposed to the risk of diseases such as white spot syndrome virus (WSSV) and Vibrio infections due to stress and a weakened immune system [6,7]. While dissolved oxygen, pH, and nitrogenous compounds are commonly monitored, there is an oversight in the role of trace elements such as zinc, magnesium, and iron. Elevated zinc and low magnesium levels have been related to oxidative stress and metabolic imbalances in shrimp, but the systematic monitoring of these parameters is still insufficient across the culture cycles. Moreover, intensive farming practices lead to nutrient buildup, later on harming nearby ecosystems, which raises awareness about the long-term sustainability of shrimp aquaculture [8]. Intensive farming practices, such as high stocking densities and overfeeding, contribute to uneaten feed and fecal accumulation, leading to eutrophication [5]. In Malaysia’s west coast ponds, algal blooms and oxygen crashes have been reported due to such practices [9].

Proper water quality management is crucial in shrimp aquaculture, as factors including temperature, pH, salinity, dissolved oxygen (DO), and nitrogen-based wastes will directly impact the shrimp growth, survival, and immune function [10,11]. These parameters are related, and maintaining a balanced environment is a must for shrimp health and aquaculture system stability [12,13]. Studies have already shown that poor water quality can lead to nutrient accumulation and algal blooms, which impose physiological stress on aquatic organisms and make them more susceptible to disease. These conditions in shrimp have been related to abnormalities like shortened antennae, gill deformities, and hepatopancreatic damage, particularly in semi-closed or recirculating systems [14,15]. Dissolved oxygen, ammonia, and salinity, which are the environmental parameters for shrimp pond farming, are critical to shrimp health, as these parameters will affect the survival, growth, and immune response [16,17]. For optimal shrimp performance, the recommended ranges are as follows: DO ≥ 5 mg/L, ammonia < 1.0 mg/L, nitrite < 0.3 mg/L, nitrate < 5 mg/L, and pH between 7.5 and 8.5 [2,18]. Readings of key water parameters such as temperature, DO, pH, and salinity that are out of the optimal range can have bad impacts on shrimp, as they will change the shrimp’s metabolic rates, disturb ion regulation, and affect microbial community dynamics. These imbalances also influence the rate of organic matter decomposition and ammonia excretion, potentially leading to oxygen depletion and environmental stress [18]. The combined effect of these stressors can create a synergistic burden on shrimp health, ultimately compromising growth, immune function, and survival [19].

Water supply sources in major urban centers have been observed to be contaminated [9]. The buildup of trace elements in aquatic animals like fish and shrimp from polluted rivers and ponds can pose a risk to human health, as these species are part of the human diet. Accumulation of trace metals in shrimp ponds has been recorded in Indonesia [20] and Vietnam [21], with zinc and manganese being the most commonly detected elements. Shrimp, which are the organisms that are at a higher position in the aquatic food chain, are known for their characteristic of collecting heavy metals in their body tissues. Consequently, it is critical to examine trace element concentrations in aquaculture water sources. Given shrimp’s nutritional and economic importance in the human diet, such monitoring is critical to preventing the transmission of harmful metal levels to consumers [22].

Despite the well-established importance of water quality in shrimp aquaculture, the specific interrelationships among individual physicochemical parameters and their role in disease occurrences remain insufficiently understood. Although trace element accumulation and interactions have been previously documented in shrimp pond environments, their temporal behavior, particularly within semi-intensive culture systems in Malaysia, has not been thoroughly investigated. This study aimed to assess water quality and trace metal ion element dynamics in an earthen shrimp pond during a 56-day culture period and to relate these trends to shrimp growth and performance. While direct physiological or health performance metrics (e.g., immune biomarkers) were beyond the scope of this study, the findings offer a foundation for environmental monitoring programs and practical management strategies.

2. Materials and Methods

Ethics statement. All animals used in this experiment were treated humanely, according to the approved procedures and guidelines of the Universiti Putra Malaysia Animal Ethics Committee guidelines (approval number: UPM/IACUC/AUP-R012/2025). We also followed the relevant guidelines and regulations for caring for the animals during this experiment.

2.1. Study Site and Sample Collection

This study was conducted in a commercial shrimp farm located near the Langat River, Selangor, Malaysia, at coordinates of 2°50′56.5″ N, 101°25′35.9″ E. Figure 1a,b show the study site of shrimp ponds and the pond used for shrimp, water quality, and trace element sampling in this study. The farm employed a semi-intensive culture system. The trial lasted 56 days, from February to April 2025. The site layout and sampling points are shown in Figure 1a,b. The semi-intensive practices, stocking density, and feed protocols used are representative of small-scale farms in West Malaysia, allowing generalizability of findings [4]. The culture pond has an approximate size of 0.3 km². The pond was equipped with a paddlewheel aerator to maintain optimal water circulation. The sources of the culture pond’s water were supplied from the Langat River. A 100-meter pipeline was constructed to connect the two water bodies and equipped with a gasoline water pump and mechanical filtration system. The river water was filtered to remove the suspended solids, organic debris, and sediments before loading into the culture ponds. This method ensures reduction in organic loads, reduces the risk of clogging, and limits the entry of the shrimp’s natural predator from the river. The turbidity level of the water was measured before and after filtration using a Secchi disk, showing a reduction of 90% in visible suspended matter. Water quality parameters of river water were continuously monitored to ensure the parameters were suitable for L. vannamei culture. A total of 220,000 post-larval white shrimp (L. vannamei, PL23) were stocked into the pond at the start of the culture cycle. Shrimp were fed commercial pellets at approximately 3% body weight daily, adjusted based on biomass estimations.

Water quality samples were collected from three designated points within the pond at five intervals: Days 0, 14, 28, 42, and 56 post-stocking, spanning a complete culture period from February 6 to April 9, 2025. These intervals were selected to correspond with key developmental stages in the shrimp growth cycle so as to evaluate temporal variations and identify potential stressors within the culture system. As part of this investigation, shrimp samples will be collected using nets or traps at predetermined intervals. Sampling will involve randomly selecting individual shrimp or collecting samples from specific areas within the pond to ensure representative data. Shrimp samples were weighed, counted, and measured to assess growth performance parameters, such as weight gain, survival rate, and size distribution.

All measurements were performed in triplicate per sampling point to ensure analytical reproducibility and support calculation of standard error. The Langat River, a major source of potable water in Selangor, supplies drinking water to nearly one-third of the state’s population [23]. However, like many other rivers in Malaysia, the Langat River is increasingly burdened by pollution, raising concerns for both human and aquaculture-related water use [24]. The Langat River is impacted by industrial discharges, agricultural runoff (notably fertilizers), and domestic sewage [23]. Given Selangor’s status as the most densely populated and rapidly developing state in the country, the environmental pressures on this transboundary river highlight the urgency of integrating water quality monitoring into aquaculture management strategies.

2.2. Physicochemical of Water Quality

Before sample collection, all the sampling bottles (1 L) were thoroughly washed, dried, and rinsed with the same water to be collected in the ponds. Collected samples were kept in cold storage and stored in the dark. The physicochemical water quality parameters, such as temperature, salinity, dissolved oxygen (DO), and pH, were recorded with a YSI Professional Plus Multi-Meter (YSI Inc., Yellow Springs, OH, USA). Furthermore, an Hach DR8000 spectrophotometer was used to measure the total ammonia nitrogen (TAN) (Hach method 8155), nitrite-N (Hach method 8507), and nitrate-N (Hach method 10049). All analyses were performed in triplicate, and data were expressed as mean ± standard deviation.

2.3. Metal Ion Analysis

Stock solutions of Zn, Cu, Mg, Mn, and Fe (1000 ppm) were prepared in 250 mL volumetric flasks and diluted using deionized water. From these, working solutions were obtained by serial dilutions to concentrations ranging from 0.5 to 5 mgL⁻¹. In our study, the calibration standards were made using a standard solution comprising 100 mgL⁻¹. Linearity was established by plotting the analyte concentration against the response peak area with linear regression analysis. Calibration procedures for all probes and spectrometers are described in Supplementary Materials. Table S1 (Supplementary Materials) was employed to establish the calibration ranges for each trace element reference. Each 50 mL water sample was transferred to a flask and filtered.

Metal ion concentrations in the sample solution were determined using a calibration curve. Calibration curves for each metal were generated using a five-point regression, with concentrations plotted against absorbance signals obtained by atomic absorption spectrophotometry (AAS, Thermo Scientific ICE 3000 v1.30, Waltham, MA, USA). Linearity was verified with regression coefficients (R² ≥ 0.995). The instrument was equipped with a deuterium background corrector, and WinLab32 software (v5.2) was used for analysis. Non-detected values were reported as <LOD (limit of detection), determined as three times the standard deviation of replicate blank readings divided by the calibration slope (LOD = 3σ/m) [25].

The concentration of trace metals in water samples was calculated according to the following expression:

$$\mathrm{C}\mathrm{x}={\displaystyle \frac{(\mathrm{A}\mathrm{x}-\mathrm{b})}{\mathrm{m}}}$$

where Cx is the concentration of the analyte (mg L⁻¹), Ax is the absorbance of the sample, m is the slope of the calibration curve, and b is the intercept. All analyses were performed in triplicate, and results are expressed as mean ± standard deviation.

2.4. Shrimp Growth Performance

To calculate the growth performance parameters, the following formulas were applied as follows:

$$\begin{array}{c}\mathrm{Shrimp} \mathrm{survival} (\%) = \left[(\mathrm{i}\mathrm{n}\mathrm{i}\mathrm{t}\mathrm{i}\mathrm{a}\mathrm{l} \mathrm{s}\mathrm{h}\mathrm{r}\mathrm{i}\mathrm{m}\mathrm{p} \mathrm{s}\mathrm{t}\mathrm{o}\mathrm{c}\mathrm{k}\mathrm{e}\mathrm{d}-\mathrm{F}\mathrm{i}\mathrm{n}\mathrm{a}\mathrm{l} \mathrm{s}\mathrm{u}\mathrm{r}\mathrm{v}\mathrm{i}\mathrm{v}\mathrm{i}\mathrm{n}\mathrm{g} \mathrm{s}\mathrm{h}\mathrm{r}\mathrm{i}\mathrm{m}\mathrm{p})/(\mathrm{i}\mathrm{n}\mathrm{i}\mathrm{t}\mathrm{i}\mathrm{a}\mathrm{l} \mathrm{s}\mathrm{h}\mathrm{r}\mathrm{i}\mathrm{m}\mathrm{p} \mathrm{s}\mathrm{t}\mathrm{o}\mathrm{c}\mathrm{k}\mathrm{e}\mathrm{d})\right]\times 100\hfill \\ \mathrm{Specific} \mathrm{growth} \mathrm{Rate}, \mathrm{SGR} (\%)=\left[(\mathrm{L}\mathrm{n}\mathrm{W}\mathrm{f}-\mathrm{L}\mathrm{n}\mathrm{W}\mathrm{i})/\mathrm{T}\right]\times 100\hfill \\ \mathrm{Feed} \mathrm{conversion} \mathrm{ratio}, \mathrm{FCR}=\mathrm{Total} \mathrm{dry} \mathrm{feed} \mathrm{intake} \left(\mathrm{g}\right)/\mathrm{Total} \mathrm{wet} \mathrm{weight} \mathrm{gain} \left(\mathrm{g}\right)\hfill \end{array}$$

where LnWf = natural logarithm of final weight, LnWi = natural logarithm of initial weight, and T = number of days of feeding trial.

2.5. Statistical Analyses

Pearson correlation analysis was performed between water quality parameters and metal concentrations. Normality and homogeneity were verified using Shapiro–Wilk and Levene’s tests. One-way ANOVA was used to determine significant differences over time (p < 0.05). All values are presented as mean ± standard error (SE), and statistical significance was set at p < 0.05.

2.6. Correlation Analysis

A correlation heatmap was constructed to explore the interrelationships among key water quality parameters measured throughout the 56-day culture period. The correlation matrix applies to a color gradient to show the strength and direction of relationships between variables. Red tones indicate strong positive correlations, blue tones represent strong negative correlations, and white corresponds to little or no correlation. The correlation values range from −1, representing a perfect negative relationship, to +1, representing a perfect positive relationship, while a value of 0 indicates no linear association. This study was limited to monitoring environmental water quality along with shrimp growth and survival, without including biological endpoints such as immune parameters. However, these environmental data are intended as a baseline for ongoing trials currently underway to investigate health and physiological responses under similar farming conditions. Pearson correlations were calculated for all parameter pairings, with Spearman rank correlations included to account for non-normality and outliers at small sample sizes. To take into consideration for multiple testing, p-values were modified using Bonferroni and Benjamini–Hochberg (FDR-BH) techniques. Effect sizes (Pearson’s r, Spearman’s ρ), raw and adjusted p-values, and Fisher z-based 95% confidence intervals for Pearson’s r are included.

3. Results

3.1. Physicochemical Water Quality Performance During Culture Period

From

Table 1. Physicochemical parameters of the shrimp pond water samples over the 56-day culture period (mean ± standard deviation).

Days of Culture	Temperature (°C)	pH (1–14)	Salinity (gL−1)	DO (mgL−1)	Ammonia (mgL−1)	Nitrite (mgL−1)	Nitrate (mgL−1)
Day 0	29.93 ± 0.15	8.71 ± 0.02	6.77 ± 0.15	6.99 ± 0.27	1.22 ± 0.02 ‡	0.05 ± 0.01	3.64 ± 1.08
Day 14	29.90 ± 0.10	7.78 ± 0.03	6.94 ± 0.02	5.09 ± 0.32	0.07 ± 0.01	0.02 ± 0.01	1.03 ± 0.12
Day 28	31.07 ± 0.15	7.66 ± 0.05	6.90 ± 0.07	4.86 ± 0.04 †	0.31 ± 0.03	0.07 ± 0.01	1.79 ± 0.23
Day 42	29.67 ± 0.15	7.58 ± 0.02	7.18 ± 0.04	4.38 ± 0.06 †	1.16 ± 0.30 ‡	0.20 ± 0.17	3.83 ± 0.20
Day 56	29.57 ± 0.31	8.69 ± 0.07	7.54 ± 0.02	6.11 ± 0.87	1.29 ± 0.14 ‡	0.10 ± 0.02	3.11 ± 0.02
Acceptable range	28–32 °C [18]	7.5–8.5	5–25	≥5 [18]	<1 [18]	<0.3 [18]	<50 [15]

† Below recommended DO threshold (≥5 mg L⁻¹) → risk of hypoxic stress. ‡ Above recommended ammonia threshold (<1.0 mg L⁻¹) → potential sublethal stress.

of the profile of water quality parameters for the 56-day shrimp culture period, the overall parameters of the water remained within acceptable ranges for L. vannamei culture. However, a few parameters showed a trend that should be highlighted involving the management concerns. The water temperature remained stable at 29.9 °C on average throughout the study period. For the pH parameter, there was a noticeable decrease from 8.71 on Day 0 to 7.75 by Day 14, which was caused by lime treatment in the pond before the introduction of shrimp. The sudden increase in biological activity or organic load also contributed to the decline in pH. The salinity showed a gradual increase from 6.60 gL⁻¹ to 7.52 gL⁻¹, which remained within the optimal range for shrimp culture. The DO levels showed a declining trend in the middle of the cycle, where they decreased from 6.99 mgL⁻¹ on Day 0 to 4.30 mgL⁻¹ by Day 42, before recovering to 6.11 mgL⁻¹ by Day 56 because of partial harvest and paddlewheel introduction. The decline of DO can be explained by the increase in shrimp biomass and organic matter decomposition as the shrimp grow into adults. Ammonia concentrations also showed similar trends where the fluctuations kept increasing during the culture period, ranging from 0.07 to 1.29 mgL⁻¹ because of similar reasons. The increase in organic matter and feed introduction will increase the microbial nitrification activity in water. The nitrite level showed a variation between 0.02 and 0.20 mgL⁻¹, with the peak level recorded on Day 42, when the shrimp had already reached adult size (Table 1) before partial harvest. The nitrate also showed a similar trend, ranging from 1.03 to 3.83 mgL⁻¹ because of similar causes. The high level of ammonia, nitrite, and nitrate on Day 0 was not a concern because it showed an effective pond fertilization to improve life food in the pond during pond preparation. The continuous monitoring of DO and nitrogenous compounds is crucial to ensure the optimal pond conditions and reduce physiological stress on cultured shrimp. Significant temporal differences were found in DO (p < 0.01), ammonia (p = 0.03), and nitrate (p = 0.02) using one-way ANOVA.

3.2. Assessment of Metal Ion During Culture Period

The metals selected (Zn, Cu, Fe, Mg, and Mn) were chosen based on their known physiological relevance in shrimp osmoregulation, immune response, and aquafeed formulations [26,27].

Table 2. Metal ion concentration in the shrimp pond water samples over the 56-day culture period. * LOD = limit of detection.

Days of Culture	Cu (mgL−1)	Zn (mgL−1)	Fe (mgL−1)	Mg (mgL−1)	Mn (mgL−1)
Day 0	<LOD	0.80 ± 1.12 *	<LOD	10.67 ± 0.01 Φ	<LOD
Day 14	<LOD	0.28 ± 0.33	<LOD	10.71 ± 0.01 Φ	<LOD
Day 28	<LOD	0.60 ± 0.35 *	<LOD	10.72 ± 0.01 Φ	<LOD
Day 42	<LOD	0.69 ± 0.66 *	0.13 ± 0.17	10.44 ± 0.36 Φ	<LOD
Day 56	<LOD	1.00 ± 0.78 *	0.01 ± 0.03	10.70 ± 0.01 Φ	0.01 ± 0.01

* Zn above recommended threshold (0.05–0.30 mgL⁻¹; [12]) → risk of osmoregulatory stress and molting disruption. Φ Mg consistently below recommended range (30–100 mgL⁻¹ [12]) → potential osmoregulatory deficiency.

depicts the temporal distribution of trace elements measured in the shrimp pond water throughout the 56-day culture period. The trace metal ions analysis showed that the Cu and Mn concentrations in pond water remained below the detection limit (<LOD) throughout the 56-day culture period. The Zn concentrations ranged from 0.28 to 1.00 mg L⁻¹, while Mg concentrations remained stable between 10.44 and 10.72 mg L⁻¹. Fe concentrations were detected at low levels, varying from 0.01 to 0.13 mg L⁻¹.

3.3. Shrimp Growth Performance

At the end of the 56-day culture period, the shrimp mean body weight increased from 3.65 × 10⁻⁵ g to 13.43 g at harvest (56 days), and the mean length increased from 2.35 cm to 13.67 cm. Average daily gain (ADG) was 0.240 ± 0.013 g, with an SGR of 23.11 ± 0.98% (

Table 3. Mean body weight, length, average daily gain, and specific growth rate of the 56-day cultured whiteleg shrimp.

	Shrimp Weight (g)	Shrimp Length (cm)
Day 0	3.65 × 10−5 ± 1.70 × 10−5	2.35 ± 0.530
Day 14	0.994 ± 0.294	4.93 ± 0.189
Day 28	5.201 ± 0.624	6.91 ± 0.870
Day 42	7.392 ± 0.933	9.24 ± 0.506
Day 56	13.430 ± 0.731	13.67 ± 0.973
Average Daily Gain (ADG)	0.240 ± 0.013	0.202 ± 0.023
Specific Growth Rate (SGR)	23.107 ± 0.977	-

). The length–weight relationship and log length–weight relationship of cultured whiteleg shrimp for 56 days are shown in Figure 2a,b. A substantial positive allometric growth pattern was observed when the length–weight relationship of cultured L. vannamei was initially analyzed using log-transformed linear regression and a conventional power function (b = 7.0381, R² = 0.8001). This suggests that during the early to mid-culture phases, shrimp developed weight disproportionately more quickly than length. A more comprehensive analysis, however, demonstrated that weight gain in relation to length slowed down in the latter phases (Days 42–56), indicating that the biological growth trajectory might not be adequately captured by a simple power-law model. In order to incorporate this into consideration, we further analyzed the data using a logistic approximation that comprised the sigmoidal growth pattern typically observed in shrimp cultivation and offered a more physiologically accurate match. The logistic function, which reflected physiological and environmental development limitations, provided a more accurate description of the rapid growth period until Day 28 and the following plateau as shrimp approached maturity.

Based on the bar graph (Figure 3), the condition factor at Day 0 was extremely low (0.00034). The condition factor rose significantly in 28 days. However, the optimum condition of shrimp culture started to decline after Day 28. The survival rate of L. vannamei was recorded at 77.8%, with 171,262 shrimp harvested from an initial stocking density of 220,000 individuals. This value indicates a relatively high survival rate under semi-intensive culture conditions. Feed efficiency was calculated using the food conversion ratio to evaluate the utilization of pelleted feed throughout the production cycle. A total of 2496.24 kg of commercial pellets were administered, resulting in a final shrimp biomass of 2314 kg. The calculated FCR was 1.08, indicating efficient feed conversion under the prevailing water quality and management practices.

3.4. Correlation Matrix Between Physicochemical Water Quality Parameters and Metal Ions

The correlation heatmap (Figure 4) revealed several clear patterns that showed a possible chemical and biological relationship within the pond ecosystem. The strongest negative correlation was between iron (Fe) and magnesium (Mg) concentrations (r = −0.9874). This inverse relationship may be due to competition between the two minerals for uptake by organisms or changes in sediment chemistry that favor one over the other. Magnesium also showed a strong negative correlation with nitrite (NO₂⁻) levels (r = −0.8788). It may be caused by ionic competition or microbial processes that regulate nitrogen compounds. Some of the parameters also exhibit positive correlation. Dissolved oxygen (DO) and pH had a strong positive correlation (r = 0.9460). It can be explained by the photosynthesis of microalgae and plants, which increases both oxygen levels and pH during daylight. Ammonia (NH₃) and nitrate (NO₃⁻) were also highly correlated (r = 0.9525). An active nitrification process occurs all the time in a high-intensive culture pond, where ammonia is converted to nitrite and then to nitrate under oxygen-present conditions. The biogeochemical processes in shrimp ponds, including mineral interactions and nitrogen cycling, are an important key relationship to understanding water quality and applying targeted interventions to protect shrimp health and maintain pond productivity.

After adjusting for multiple comparisons using either Bonferroni or FDR-BH at α = 0.05, no associations were still statistically significant across all pairwise tests. Given the small sample size (n = 5) and the numerous comparisons, which significantly diminish statistical power, this result is to be expected. For transparency, we provide the whole set of raw and adjusted p-values and instead concentrate on the strength and direction of connections rather than rigorous significance levels. Due to the limitations on power of our small sample size (n = 5), the lack of statistically significant correlations after adjustment should not be regarded as proof of no link. We presented both Pearson and Spearman estimates to evaluate robustness, and they produced consistent patterns for the majority of parameter pairings. However, given the wide associated confidence intervals, we advise against overinterpreting the substantial apparent impact sizes.

4. Discussion

4.1. Temperature

This study focused on environmental water quality parameters as potential early indicators of pond health. However, shrimp physiological or health performance metrics (e.g., immune activity) were not included and remain a limitation. Temperature remained stable at approximately 29.9 °C across Day 0 and Day 56. This falls well within the optimal thermal range for shrimp, which is generally cited as 28–32 °C [15]. Within this range, shrimp exhibit optimal metabolic performance, reproduction, growth, and feed conversion efficiency, as well as immune responses [28,29,30]. Temperature stability is particularly critical in tropical pond systems, where changes beyond the optimal range can disrupt physiological balance, increase vulnerability to stress and disease, and affect the solubility of trace metals in the water.

4.2. pH

pH values showed a decline from 8.71 at Day 0 to 7.75 by Day 14. Even though the pH value is still within the ideal range of 7.5–8.5 (±0.5) that is recommended for shrimp culture, the downward pattern of the pH seen during the period of sampling suggests an increase in biological activity and organic load inside the pond [31,32,33]. The decrease in pH of a culture pond can increase the microbial respiration rate, resulting in elevated CO₂ levels during nighttime. It may also reduce photosynthesis because of the mass mortality of phytoplankton [34]. Further acidification of the pond water can negatively impact the molting exoskeleton, osmoregulation, and enzyme function of cultured shrimp.

4.3. Salinity

The salinity value shows a mild increase in trend from 6.60 gL⁻¹ to 6.92 gL⁻¹, which is still within the acceptable range for shrimp culture. Shrimp culture has been found to be optimal in 10–25 gL⁻¹; however, it can tolerate salinity between 5 and 40 gL⁻¹ [28,35,36]. During the dry season, reduced freshwater inflow leads to a slight increase in salinity, which can induce osmotic stress in juvenile shrimp; thus, maintaining salinity within standardized limits is crucial to prevent stress from sudden changes in water conditions. Although seasonal influences were not measured directly, observed salinity changes may reflect dry-season evaporation and limited inflow.

4.4. Dissolved Oxygen (DO)

The DO level of the pond showed a significant decline from 6.99 mgL⁻¹ on Day 0 to 4.92 mgL⁻¹ on Day 14, approaching the lower value threshold for shrimp culture minimum DO level. The recommended minimum level for DO in shrimp culture is 5.0 mgL⁻¹ to prevent sublethal stress [31,37]. Additional aeration was introduced after Day 14 to mitigate DO stress, including extending paddlewheel hours from 10 to 14 h per day. The decrease in dissolved oxygen can result from the increase in shrimp growth and microbial activity, excessive feeding, organic matter decomposition, and poor aeration. This can increase mortality and low feed intake at night because oxygen is severely depleted. Fluctuations in DO and pH were closely linked to photosynthetic activity and organic matter decomposition. However, proper aeration and feed management, together with the reduction of organic matter, will help to achieve stability of oxygen in water.

4.5. Ammonia, Nitrite, and Nitrate

Ammonia, nitrite, and nitrate concentrations in the pond system are very important parameters that represent the health of nitrogen metabolism. These three compounds relate to each other through various biotic and abiotic chemical processes to complete a process called the nitrogen cycle. Each of the compounds can significantly affect the shrimp culture’s health if not properly managed and elevated beyond the threshold of a toxic level. The ammonia levels have fluctuated during the shrimp culture period, elevating from 0.07 to 1.29 mgL⁻¹. An increase in ammonia value above 1.0 mgL⁻¹ can cause a sublethal stress in cultured shrimp because of an increase in unionized ammonia (NH₃). Unionized ammonia is very toxic to shrimp since it causes damage to gill function and hepatocyte function, reduces growth, and decreases food intake. High ammonia readings that were observed in the early and middle phases of culture may have been caused by overfeeding of the shrimp culture or insufficient microbial activity to break down shrimp waste for the nitrification process. Ammonia and nitrite spikes reflected imbalances in the microbial nitrogen cycle, highlighting the importance of managing pond aeration and organic load.

The total ammonia concentrations for shrimp culture should be maintained below 1 mgL⁻¹ in order to maintain shrimp well-being [18]. The nitrite concentration should be maintained in a range of 0.02 to 0.40 mgL⁻¹. A sudden elevation of nitrite concentration during mid-cycle (0.40 mgL⁻¹) may cause nitrite toxicity, presenting with the formation of methemoglobinemia in shrimp hemolymph, which reduces the oxygen transport in the shrimp circulatory system. Prolonged exposure to nitrite levels above 0.1 mgL⁻¹ has been shown to be lethal for shrimp, especially when cultured in low salinity settings for an aquaculture system [33]. The spike of nitrite during the culture may be caused by the imbalance in nitrifying bacterial population activity, such as Nitrosomonas (converts ammonia to nitrite) and also Nitrobacter (converts nitrite to nitrate). The end product of pond nitrogen metabolism, nitrate, is known as less toxic, and the safety range recommended is from 0.90 to 4.27 mgL⁻¹. The increase in nitrate in the reading of the shrimp ponds gives an indicator that the nitrification process has resumed normally. The presence of nitrate in shrimp culture suggested that the biofilter or pond microbial community is functioning normally as intended. The elevated levels of nitrate with high ammonia could point to pond system overloading or incomplete nitrification.

The interaction between ammonia, nitrate, and nitrite, which undergo the nitrification process together with microbial health, is shown in Figure 5. The higher the ammonia level rises, the higher the concentration of nitrite. This can cause nitrification, in which the bacteria undergo oxidation of ammonia to nitrite. The concentration of nitrite shown, 0.40 mgL⁻¹, can also cause the Nitrobacter species to convert nitrite into nitrate. The accumulation of nitrite is not aligned with the increase in nitrate. This can delay the oxidation of nitrite. Microbial processes can be interrupted by higher organic content, low temperature, and dissolved oxygen. It can still be converted partially even in higher concentrations of nitrite [18].

4.6. Metal Ion Concentration

Management of water quality can be improved with better aeration and feeding regimes to ensure stability and efficiency of nitrifying bacteria. The World Health Organization and the Department of Environment, Malaysia, have set the limit of the concentrations of metal ions, including Cu, Zn, Mn, Fe, and Mg, which help in shrimp health and microbial community [38,39].

The consistent <LOD value of Cu and Mn inside the pond during the study period indicates the negligible contribution of these elements towards the pond’s ionic composition. However, this composition reading is valuable for the development of a baseline condition comparison for future analysis of environmental changes in pond culture. Zn and Mg concentrations remain within the ranges of the reported values for the semi-intensive systems. However, the upper Zn values (~1.00 mg L⁻¹) and relatively low Mg levels (~10.44 mg L⁻¹) need to be addressed since previous studies have linked the elevated Zn exposure and low Mg availability to potential physiological stress in L. vannamei via impaired osmoregulation and oxidative stress [40,41].

In this present study, the assessment of shrimp behavior and direct physiological parameters is not measured. Therefore, our interpretations regarding stress are hypothesized based on established literature rather than observed evidence. The research in the future should incorporate the water quality measurements with shrimp behavioral monitoring and hemolymph ion analysis to verify the connections between environmental conditions and shrimp physiology. Cu levels were consistently below detection limits across all pond samples, suggesting minimal contamination or background levels well within safe thresholds. This is ideal, as excessive Cu²⁺, especially in soft or low-salinity water, can impair shrimp gill function and microbial nitrification. Conversely, Zn concentrations varied significantly, with several samples exceeding 1.0 mgL⁻¹, well above the recommended safety threshold of 0.3 mgL⁻¹ for shrimp. Based on Boyd (2020) and FAO [12,42] guidelines, Zn²⁺ levels range from <0.05 to 0.3 mg/L, where above 0.3 mg/L can be toxic to shrimp, especially in soft water or low salinity conditions, where Zn²⁺ is more bioavailable. Previously, Zn concentration was significantly higher among heavy metals reported in water shrimp ponds in the north coast of Central Java and the Gulf of Mannar, ranging from 49 to 681 μg L⁻¹ and 0.57 to 4.27 μg L⁻¹, respectively [20,43]. Elevated Zn levels may stem from Zn-rich feed additives or runoff and could potentially disrupt osmoregulation, enzyme function, and molting [44,45]. Elevated Zn levels may stem from Zn-rich feed additives or runoff and could potentially disrupt osmoregulation, enzyme function, and molting.

The shrimp farm ponds in Vietnam have lower concentrations of 0.28 mgL⁻¹ of Mn and 1.36 mgL⁻¹ of Fe, respectively [21]. This study, however, found these concentrations are lower than those observed in Vietnam. Lower Fe levels may be attributed to reduced sediment resuspension, different feed formulations, and higher pH, which reduces Fe solubility. Both heavy metals assist in the degradation of microbes in pond sediments. It can process in natural aquatic environments. However, this condition caused oxygen deficiency at the pond bottom, reducing the insolubility of Mn and Fe. The condition will then lead to the other metal ion concentrations in the pond water [46,47,48]. Reduction of Mn as an essential micronutrient causes it to become toxic in water and opposes the immune function, osmoregulation, and ion retention [27,48]. Mn helps in shrimp’s exoskeleton and neuromuscular function [49,50]. This is contrary to the Fe, which is already low within the standard. Fe itself contributes to the metabolism of energy, transportation of oxygen, and shrimp’s immune responses [51]. It should be in control, as the presence of iron ions can potentially cause anaerobic conditions in water. This can deteriorate the shrimp’s health, as it can appear to be stressed and have an obstruction of the gills. One culture period showed a non-optimal range of Mg, 10.4 mgL⁻¹ to 10.7 mgL⁻¹, which has been recorded as the range should be 30.0–100.0 mgL⁻¹ in shrimp culture. The low range of Mn can deteriorate shrimps’ health in a low-salinity pond with limited mineral content.

These metal ion results are stable, but two main issues are coming from higher levels of Zn and lower levels of Mg. Two of the trace elements need to be managed properly to improve shrimp’s health and environmental stability. Trace element analysis showed that zinc levels approached thresholds that may impair shrimp health, while consistently low magnesium concentrations could contribute to osmoregulatory stress. Negative correlations between magnesium and both iron and nitrite suggest competitive uptake or inhibitory interactions in pond systems. These trends should therefore be interpreted as preliminary and warrant follow-up investigation. The consistent trends observed among DO, nitrogen compounds, and trace metals suggest that such interactions may precede detectable health effects, which warrants further investigation involving physiological and immunological endpoints.

4.7. Shrimp Growth Performance

In this study, we found that the condition factor at Day 0 was extremely low (0.00034) because the shrimp were still in the larval stage, and the body morphology tends to elongate the frame compared to juveniles and adults. The condition factor rose significantly in 28 days, indicating the optimal condition for shrimp culture in terms of growth. A large variation in individual shrimp conditions has been found in this period, indicating some of the shrimp are not thriving well. In this stage, we can infer that the nutrient absorption of shrimp is most efficient. The environment and the feeding strategies are most suitably matched to shrimp growth needs. Under semi-intensive pond environments, L. vannamei gained weight substantially quicker than length, as indicated by this study’s positive allometric growth (b = 7.28 in the power model). In various settings, earlier research has shown lower b values that are typically in the isometric range (b = 3.0). For instance, b = 3.14 was reported in intensive pond systems in Mexico [52], while b values ranging from 2.9 to 3.3 were reported for L. vannamei raised at low salinity in China [2]. Similarly, shrimp cultivated in Brazil using biofloc technology showed positive but moderate allometry (b = 3.4) [15]. Our study’s significantly higher b value could be explained by its rapid biomass gain in the early- to mid-culture stages as well as nutrient-rich pond conditions and management approaches. Nonetheless, the logistic function’s better description of the subsequent slowdown in weight gain in relation to length after Day 28 points to density or environment-related growth restrictions as culture advanced. These comparisons demonstrate the way salinity, culture system, stocking density, feed type, and water quality each have an influence on L. vannamei’s LWR, which is very dependent on the environment. Although the high b value presented here serves as a guide for Malaysian semi-intensive tropical ponds, it also emphasizes the necessity of multi-site comparisons in order to create regional standards.

However, the optimum condition of shrimp culture started to decline after Day 28. The losing condition can be explained by several biological factors, such as overcrowding and competition as shrimp grow larger, molting stress occurring, and the energy of shrimp being shifted from growth to reproduction as shrimp mature. Overcrowding stress can further reduce access to food and cause aggression or cannibalism among the shrimp [53,54]. During the molting phase at mid-to-late culture, shrimp energy is allocated toward the molting process, and dry mass also starts to reduce as exoskeleton detachment occurs later [55,56,57]. Environmental factors also play a role in this case; when ammonia builds up, oxygen and pH fluctuations can induce environmental stress in shrimp. As the pond biomass is increased, the ammonia compound waste and organic load will surely increase as the pond volume remains the same. The same story goes for oxygen concentration in the pond water. If not well managed, it will cause a loss in conditioning as toxicity increases and suboptimal dissolved oxygen, as we can see in the case above. Even though the length–weight relationship shows a positive allometric, the drop in condition factors showed that a significant reduction in the rate of weight gain occurs relative to the size of the shrimp. A good strategy can be implemented to manage this problem, such as a partial harvest 42 days before, adjusting the feeding rate accordingly, and assessing water parameters and shrimp condition weekly. Although shrimp achieved acceptable growth and feed efficiency, reduced survival (77.8%) may be partially attributed to DO stress and metal ion imbalance. Our findings support the need for integrated monitoring of both traditional water quality parameters and traces of metal ions to identify early warning signs of pond deterioration.

5. Conclusions

This study provides foundational environmental baseline data on nutrient–metal interactions within shrimp pond systems. The temporal findings of trends in shrimp performances and water parameters suggest a potential environmental stress indicator, although direct physiological parameters were not assessed. Water quality monitoring should be incorporated with physiological assessments such as immune enzyme activity, histopathology, and growth performance. Integrated approaches will further enhance the understanding of the aquaculture system and support more sustainable shrimp farming practices.

Limitations and Future Directions

This study was conducted in a single pond during the dry season and did not assess shrimp physiological or immune responses. Future work should integrate biochemical and immunological biomarkers to establish direct causal links between water quality fluctuations and shrimp health.