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Advancing Applications in Hydrogeochemical Processes in Groundwater Systems

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A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Hydrology".

Deadline for manuscript submissions: 20 July 2026 | Viewed by 11059

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Dr. Jason Polk

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Guest Editor

Department of Earth, Environmental, and Atmospheric Sciences, Western Kentucky University, Bowling Green, KY, USA
Interests: karst hydrology; groundwater modeling; water resource management; isotope hydrology; hydrogeochemistry
Special Issues, Collections and Topics in MDPI journals

Dr. Nenad Marić

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Guest Editor Assistant

Department of Ecological Engineering, Faculty of Forestry, University of Belgrade, Belgrade, Serbia
Interests: hydrogeology; hydrochemistry; groundwater quality; groundwater contamination; non-aqueous phase liquids; monitored natural attenuation; bioremediation

Special Issue Information

Dear Colleagues,

The study of hydrogeochemical processes in groundwater systems plays a pivotal role in understanding the quality, availability, and sustainability of water resources. Recent advancements in analytical techniques and computational modeling have significantly enhanced our ability to predict and manage groundwater chemistry. Moreover, integrating geochemical data with hydrological models provides a holistic approach to groundwater management, essential for addressing global challenges such as water scarcity, pollution, and climate change. Advancing applications in hydrogeochemical processes in groundwater systems cover a wide range of areas, including, but not limited to, contaminant transport and remediation, nutrient pollution, biogeochemical cycling, isotopic and geochemical tracing, emerging contaminants and water quality concerns, machine learning and big data in hydrogeochemistry, predictive modeling, and applications in karst groundwater systems. As the demand for clean groundwater increases, advancing applications in hydrogeochemical processes become indispensable for sustainable water resource management and environmental protection.

This Special Issue of Water focuses on all aspects related to advancement in hydrogeochemical processes in groundwater systems.

Dr. Jason Polk
Guest Editor

Dr. Nenad Marić
Guest Editor Assistant

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Keywords

groundwater systems
hydrogeochemical processes
hydrochemistry
isotopic and geochemical tracing
emerging contaminants and water quality concerns
karst hydrology
predictive modeling
water resource management

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Published Papers (8 papers)

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Research

31 pages, 5891 KB

Open AccessArticle

Geo-AI Ensemble Modeling Framework for Assessing Groundwater Contamination Under Anthropogenic Pressures in an Extensive Peri-Urban Agricultural Aquifer to Support Sustainable Groundwater Management

by Mohamed Haythem Msaddek, Mohsen Ben Alaya, Lahcen Zouhri, Yahya Moumni and Bilel Abdelkarim

Water 2026, 18(8), 937; https://doi.org/10.3390/w18080937 - 14 Apr 2026

Viewed by 461

Abstract

Rapid urbanisation and intensified agriculture are major drivers of groundwater contamination in peri-urban agricultural aquifers worldwide. Contaminants including nitrates and phosphates accumulate through fertilizer use, wastewater infiltration, and groundwater overextraction, creating complex spatial and temporal patterns. Quantifying these impacts under multiple anthropogenic pressures remains a key challenge for effective water resource management. This study develops a Geo-AI ensemble modeling framework that integrates grid-based spatial analysis with advanced machine learning to assess groundwater contamination dynamics. A composite contamination index (CCI) was constructed to synthesize hydrochemical indicators into a unified measure of aquifer degradation. The AI framework uses Graph Neural Networks (GNNs), Light Gradient Boosting Machine (LightGBM), and Deep Long Short-Term Memory Networks (LSTM). Anthropogenic drivers include population growth, infrastructure density, agricultural intensity, groundwater abstraction, and hydroclimatic variability, providing a comprehensive understanding of contamination sources. The methodology was applied to the urbanised aquifer of Manouba, western suburban Tunis (Tunisia), using 295 samples collected from 85 monitoring wells between 2005 and 2025. Validation results show strong predictive performance, with LightGBM achieving R² = 0.986, RMSE = 13.14, and MAE = 1.72, outperforming GNNs (R² = 0.972) and LSTM (R² = 0.943). The spatial analysis reveals a major shift in contamination patterns, with severe contamination expanding to 55% of the study area in 2025, compared with 7% in 2005, while low and slight contamination declined from 45% to 20%. The results highlight how urban expansion reduces recharge, increases pollutant loading, and amplifies aquifer vulnerability, while agricultural intensification further accelerates contaminant accumulation and degradation processes. This framework provides a transferable, data-driven tool for mapping contamination hotspots and supporting targeted, sustainable groundwater management in peri-urban agricultural aquifers under increasing anthropogenic pressures worldwide. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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23 pages, 3580 KB

Open AccessArticle

Explainable Deep Learning and PHREEQC-Constrained Assessment of Genesis and Health Risks of Deep High-Fluoride Groundwater: A Case Study of Hengshui City, North China Plain

by Xiaofang Wu, Yi Liu, Haisheng Li, Fuying Zhang, Xibo Gao and Jiyi Jiang

Water 2026, 18(5), 600; https://doi.org/10.3390/w18050600 - 1 Mar 2026

Viewed by 389

Abstract

Fluoride (F⁻) contamination in deep groundwater threatens drinking water security, yet its enrichment is commonly governed by coupled nonlinear hydrogeochemical feedbacks that are difficult to resolve with linear diagnostics alone. Here, we integrate an explainable deep learning framework (HydroAttentionNet + SHAP) with thermodynamic and mass-conservative inverse modeling (PHREEQC) to quantitatively link data-driven thresholds to mineral water processes in a multi-aquifer system. Using 258 deep-well samples, we delineate a robust evolution pathway from background to ultra-high-fluoride (Ultra-High F⁻, ≥1.5 mg/L) waters. HydroAttentionNet achieves strong predictive skill (R² = 0.77) and reveals a clear mechanistic tipping behavior: alkalinity (HCO₃⁻/CO₃²⁻) is the primary trigger for F⁻ activation, while progressive Na+ enrichment and Ca²⁺ depletion act as amplifiers by suppressing a(Ca²⁺) and weakening fluorite precipitation capacity. PHREEQC simulations confirm a coupled “salinization–decalcification–fluoridation” loop in which (i) evaporite dissolution elevates ionic strength (salt effect) and supplies Na⁺ to promote Na–Ca exchange, and (ii) carbonate re-equilibration drives calcite precipitation as an efficient Ca sink, offsetting ~45.8% of Ca²⁺ inputs; together, these processes maintain fluorite undersaturation and sustain net fluorite dissolution, contributing 56.6% of newly added dissolved F⁻ in evolved end-members. Monte Carlo health risk assessment (10,000 iterations) indicates substantial intergenerational inequity: 67.9% of children exceed the non-carcinogenic risk threshold (HQ > 1), compared with 29.3% of adults. Sensitivity analysis identifies source-water fluoride concentration as the dominant driver (Spearman r = 0.93), implying that supply-side interventions (defluoridation, well-screen optimization, and blending with low-F sources) are substantially more effective than behavioral measures. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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20 pages, 5427 KB

Open AccessArticle

Historical Compilation and Hydrochemical Behavior in the Groundwater Flow System of Central Mexico

by Selene Olea-Olea, Aurora Guadalupe Llanos-Solis, Eric Morales-Casique, Priscila Medina-Ortega, Nelly L. Ramírez-Serrato, Daisy Valera-Fernández, Esperanza Torres-Rodríguez, Felipe Armas-Vargas, Lucy Mora-Palomino and Orlando Valdemar Villa-Cadena

Water 2026, 18(2), 171; https://doi.org/10.3390/w18020171 - 8 Jan 2026

Viewed by 749

Abstract

The Cuitzeo Groundwater Flow System, located in central Mexico within a volcanic rock region, encompasses two of the largest lakes in the country: Lake Cuitzeo and Lake Pátzcuaro. These lakes are sustained by both surface water and groundwater discharge, playing a critical role in local ecosystems and the surrounding population. Groundwater is particularly important for maintaining the lakes’ existence. However, the behavior of the groundwater flow system in this region has not been previously described. This study compiles historical data from 170 groundwater sites within the system from different years and includes temperature (°C), pH, total dissolved solids (TDS), major ions, and geology in detail. The historical data provide a spatial analysis and initial characterization to study the hydrochemistry of the system, identify recharge and discharge zones, assess water-rock interaction processes, and trace the evolution of groundwater. The results highlight distinct chemical behaviors across the different zones of the study area, with the most notable being ion exchange consistent with the weathering of volcanic silicates and interaction with lacustrine sediments. This study is crucial as it offers valuable insights into the hydrochemistry and water levels of the groundwater flow system and highlights areas where additional data are needed to better understand its dynamics. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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27 pages, 6323 KB

Open AccessArticle

Multivariate Analysis and Hydrogeochemical Evolution of Groundwater in a Geologically Controlled Aquifer System: A Case Study in North Central Province, Sri Lanka

by Uthpala Hansani, Sapumal Asiri Witharana, Prasanna Lakshitha Dharmapriya, Pushpakanthi Wijekoon, Zhiguo Wu, Xing Chen, Shameen Jinadasa and Rohan Weerasooriya

Water 2026, 18(1), 89; https://doi.org/10.3390/w18010089 - 30 Dec 2025

Cited by 1 | Viewed by 767

Abstract

This study investigates the coupled relationship between groundwater chemistry, lithology, and structural features in the dry zone of Netiyagama, Sri Lanka, within a fractured crystalline basement. Groundwater chemistry fundamentally reflects geological conditions determined by rock-water interactions, we hypothesized that the specific spatial patterns of groundwater chemistry in heterogeneous fractured systems are distinctly controlled by integrated effects of lithological variations, structurally driven flow pathways, aquifer stratification, and geochemical processes, including cation exchange and mineral-specific weathering. To test this, we integrated hydrogeochemical signatures with mapped hydrogeological data and applied multi-stage multivariate analyses, including Piper diagrams, Hierarchical Cluster Analysis (HCA), and Principal Component Analysis (PCA), and various bivariate plots. Piper diagrams identified five distinct hydrochemical facies, but these did not correlate directly with specific rock types, highlighting the limitations of traditional methods in heterogeneous settings. Employing a multi-stage multivariate analysis, we identified seven clusters (C1–C7) that exhibited unique spatial distributions across different rock types and provided a more refined classification of groundwater chemistries. These clusters align with a three-unit aquifer framework (shallow weathered zone, intermittent fracture zone at ~80–100 m MSL, and deeper persistent fractures) controlled by a regional syncline and lineaments. Further analysis through bivariate diagrams revealed insights into dominant weathering processes, cation-exchange mechanisms, and groundwater residence times across the identified clusters. Recharge-type clusters (C1, C2, C5) reflect plagioclase-dominated weathering and short flow paths; transitional clusters (C3, C7) show mixed sources and increasing exchange; evolved clusters (C4, C6) exhibit higher mineralization and longer residence. Overall, the integrated workflow (facies plots + PCA/HCA + bivariate/process diagrams) constrains aquifer dynamics, recharge pathways, and flow-path evolution without additional drilling, and provides practical guidance for well siting and treatment. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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24 pages, 15580 KB

Open AccessArticle

Groundwater Potential Mapping in Semi-Arid Areas Using Integrated Remote Sensing, GIS, and Geostatistics Techniques

by Ahmed El-sayed Mostafa, Mahrous A. M. Ali, Faissal A. Ali, Ragab Rabeiy, Hussein A. Saleem, Mosaad Ali Hussein Ali and Ali Shebl

Water 2025, 17(13), 1909; https://doi.org/10.3390/w17131909 - 27 Jun 2025

Cited by 5 | Viewed by 3502 | Correction

Abstract

Groundwater serves as a vital resource for sustainable water supply, particularly in semi-arid regions where surface water availability is limited. This study explores groundwater potential zones in the East Desert, Qift–Qena, Egypt, using a multidisciplinary approach that integrates remote sensing (RS), geographic information systems (GIS), geostatistics, and field validation with water wells to develop a comprehensive groundwater potential mapping framework. Sentinel-2 imagery, ALOS PALSAR DEM, and SMAP datasets were utilized to derive critical thematic layers, including land use/land cover, vegetation indices, soil moisture, drainage density, slope, and elevation. The results of the groundwater potentiality map of the study area from RS reveal four distinct zones: low, moderate, high, and very high. The analysis indicates a notable spatial variability in groundwater potential, with “high” (34.1%) and “low” (33.8%) potential zones dominating the landscape, while “very high” potential areas (4.8%) are relatively scarce. The limited extent of “very high” potential zones, predominantly concentrated along the Nile River valley, underscores the river’s critical role as the primary source of groundwater recharge. Moderate potential zones include places where infiltration is possible but limited, such as gently sloping terrain or regions with slightly broken rock structures, and they account for 27.3%. These layers were combined with geostatistical analysis of data from 310 groundwater wells, which provided information on static water level (SWL) and total dissolved solids (TDS). GIS was employed to assign weights to the thematic layers based on their influence on groundwater recharge and facilitated the spatial integration and visualization of the results. Geostatistical interpolation methods ensured the reliable mapping of subsurface parameters. The assessment utilizing pre-existing well data revealed a significant concordance between the delineated potential zones and the actual availability of groundwater resources. The findings of this study could significantly improve groundwater management in semi-arid/arid zones, offering a strategic response to water scarcity challenges. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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21 pages, 13081 KB

Open AccessArticle

Spatiotemporal Evolution and Driving Factors of Groundwater in Beijing Sub-Center

by Xiaowei Xue, Xueye Gu, Yicun Du, Ning Zhang and Shiyang Yin

Water 2025, 17(11), 1668; https://doi.org/10.3390/w17111668 - 30 May 2025

Viewed by 997

Abstract

Tongzhou District is the urban sub-center of Beijing, and the importance of groundwater resources is increasingly prominent. Based on groundwater level data from 1980 to 2020 and water usage data from various sectors in Tongzhou District between 2011 and 2020, this paper utilizes continuous wavelet transform (CWT), geostatistical models, and grey relational analysis (GRA) to explore the spatiotemporal evolution patterns and influencing factors of groundwater levels in Tongzhou District. The study reveals that the groundwater level evolution in Tongzhou District exhibits two primary cycles, and it predicts that the groundwater level at Liyuan Station will decrease and eventually rebound. From 1980 to 2020, the overall trend of groundwater levels in Tongzhou District showed a decline. However, the groundwater levels in the central and southern regions exhibited an upward trend from 2000 to 2020. The groundwater level is mainly influenced by spatial structural factors, with minimal impact from external random factors. Domestic water consumption, water usage in the tertiary sector, and industrial water usage have the greatest impact on groundwater levels, attributed to the rapid growth of the population and regional economy. Agricultural water usage has the least grey relational grade, which is related to changes in agricultural development planning in the study area, as well as reductions in the area of crop planting and the actual utilization area of facility agriculture. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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22 pages, 35380 KB

Open AccessArticle

Groundwater Quantity and Quality Management in a Mountainous Aquifer System in NE Greece

by Ismail Empliouk, Ioannis Gkiougkis, Adam Adamidis, Ilias Siarkos, Andreas Kallioras, Dimitrios Kaliampakos and Fotios-Konstantinos Pliakas

Water 2025, 17(9), 1292; https://doi.org/10.3390/w17091292 - 25 Apr 2025

Viewed by 1908

Abstract

This research work investigates the Myki Municipality’s aquifer system in the mountainous region of Xanthi Prefecture, Northeast Greece, with regard to the area’s groundwater exploitation and management requirements for drinking water supply. During the period 2021–2023, the work involved (i) groundwater discharge measurements and groundwater sampling from forty-seven (47) springs and five (5) groundwater wells, followed by groundwater chemical analyses; (ii) appropriate analysis, elaboration, and presentation of the results obtained; and (iii) formulation of related proposals that would improve the conditions of the water supply in the study area. The study revealed that water shortage circumstances exist in the study area, which may be due to low aquifer capacity in some areas, deficient groundwater recovery facilities, and water losses in the water supply network. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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16 pages, 10213 KB

Open AccessArticle

Improved Modelling Concept for Dewatering Planning in Velenje Coal Mine

by Darian Božič, Blaž Janc, Ivan Supovec and Janez Rošer

Water 2025, 17(1), 20; https://doi.org/10.3390/w17010020 - 25 Dec 2024

Cited by 1 | Viewed by 1360

Abstract

The basis for the safe extraction of mineral resources underground is good knowledge of the local and surrounding geological conditions and the activity of the nearby aquifers. Hydrogeological modelling in combination with dewatering of the aquifers above the coal and monitoring of the groundwater level in piezometers is of particular importance for safe underground coal mining in the Velenje mine. This study shows the contribution of an improved hydrogeological conceptual model to the prediction of groundwater movement in the aquifers above the coal seam using a hydrodynamic six-layer model. The improved hydrogeological conceptual model is based on the determination of the groundwater age and a detailed geological classification of the layers. The groundwater ages, determined using the tritium detection method, were important to understand the recharge of the individual aquifers. As there is no direct recharge at the surface, the aquifers are only recharged by the slow leakage of groundwater from the upper to the lower aquifers. The hydrodynamic six-layer model, which is based on an improved hydrogeological conceptual model, now simulates groundwater more accurately than previous hydrodynamic models and helps with dewatering planning and the technical design of mining facilities near aquifers. Full article

(This article belongs to the Special Issue Advancing Applications in Hydrogeochemical Processes in Groundwater Systems)

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