Indonesian Throughflow in the Halmahera Sea: A Review

Abstract

The Indonesian Throughflow (ITF) significantly influences global climate and interoceanic exchange. This review synthesizes recent findings on the Halmahera Sea’s role within the ITF, emphasizing its physical mechanisms, climatic modulation, and ecological consequences. Despite being a minor route, the Halmahera Sea transport volume is approximately 1.5 to 2.44 Sv, bringing water mass from the Southern Pacific Ocean. Seasonal and interannual variability, driven by monsoonal winds and phenomena like the El Niño-Southern Oscillation (ENSO), significantly affect the flow dynamics in this region. The Halmahera Sea also plays a pivotal role in nutrient cycling and marine biodiversity, influencing local ecosystems and fisheries. Understanding these dynamics is essential for predicting climate change impacts and managing marine resources in the Indo-Pacific region. This review highlights the need for enhanced observational efforts and high-resolution modeling to better understand the Halmahera Sea’s contribution to the broader ITF framework and its implications for regional and global climate systems.

1. Introduction

The maritime region of Indonesia exerts a substantial influence on the global climate system and interoceanic exchanges. This influence arises from the transport of water masses from the western Pacific Ocean to the southeastern Indian Ocean, driven by pressure gradients, a mechanism known as the Indonesian Throughflow (ITF) [1,2]. The ITF is a crucial oceanographic mechanism facilitating the transfer of warm Pacific waters to the Indian Ocean. This interocean exchange plays a vital role in the global climate system by affecting regional ocean currents and thermohaline circulation. The ITF is estimated to transport approximately 12–15 Sverdrups (Sv) of water, significantly influencing the thermal dynamics and climate patterns of both oceanic basins [3,4]. Through Indonesian seas, warm and low-salinity waters are transported westward, contributing to the redistribution of heat transport (ranging from 0.5 to 1.0 PW, where 1 PW = 10¹⁵ watts of power), salinity (decreasing by approximately 0.3–0.5 PSU), and biogeochemical properties (with estimates indicating that up to 0.2 teragram per year (Tg/year) of phosphorus and 0.5 Tg/year of nitrogen may be transported via the ITF) between these two basins [3,4]. Among the various routes forming this interoceanic exchange, the Halmahera Sea, located in eastern Indonesia, has garnered increasing attention due to its role as a minor yet crucial channel within the ITF system [5,6].

The ITF has two main geographical entry points into Indonesian seas: the western route through the Makassar Strait and the eastern route through the Maluku Sea and Halmahera Sea [7,8]. The primary ITF route is through the Celebes Sea and Makassar Strait, depicting the complete westward transport of Pacific waters. In addition, there is a minor pathway through the Halmahera Strait, but this appears to be a less significant or incomplete route compared to the main Makassar Strait passage (Figure 1) [7]. As shown in Figure 1, the primary inflow for the ITF passes through the Makassar Strait. The Makassar Strait carries about 80% of the ITF transport [8]; a portion of the outflow continues to the Indian Ocean via the Lombok Strait, while the majority flows eastward towards the Banda Sea before entering the Indian Ocean through the Ombai Strait and Timor Passage [9,10,11]. The second inflow is via the Halmahera Sea for South Pacific Subthermocline Water (SPSW), and a third is through the Maluku Sea for Upper Thermocline South Pacific Subtropical Water (SPSTW) [11]. This inflow is characterized primarily by SPSW. This water mass resides within the subthermocline layer and is indicated to be modified by tidal mixing and interaction with surrounding water masses [10]. In contrast, the inflow through the Maluku Sea primarily consists of Upper Thermocline South Pacific Subtropical Water (SPSTW). This water mass has distinct thermal properties and is located higher in the thermocline layer, typically measured at a depth of around 150 to 300 m [11]. This suggests that the Banda Sea and Timor Passage play an important role in the larger-scale ocean circulation and property exchanges facilitated by the ITF system (Figure 1) [8].

Figure 1. This map illustrates the bathymetric and geographic features of the ITF routes. The main route of the ITF is marked with red lines. The paths north of the Banda Sea remain unclear and uncertain. (This plot is redrawn based on [6]).

The ITF is not a single, continuous current but rather a complex system of interconnected flows passing straits, seas, and passages, including the Makassar Strait, Lifamatola Passage, Halmahera Sea, and Maluku Sea. Each contributes unique hydrographic characteristics and temporal dynamics. Specifically, the Halmahera Sea mediates part of the Pacific inflow into the Banda Sea and subsequently the Indian Ocean, with estimates suggesting it transports approximately 1.5 to 2.44 Sv of seawater [12,13].

This transport is sensitive to large-scale climate oscillations, particularly the El Niño-Southern Oscillation (ENSO), which alters wind patterns, thermocline structure, and surface salinity, influencing both the volume and direction of the flow [14,15]. The measurement period for the observational dataset typically encompasses several months to multiple years. For instance, data from the Argo float program, which provides extensive temperature and salinity (T-S) profiles, covers a wide temporal span, gathering thousands of measurements monthly across diverse geographic areas in the Indonesian seas [16,17]. Observational data also include velocity (20 m depth interval), transport, and profiles from moorings, collected over the period from 2004 to 2006 [16]. Moored data from the International Nusantara Stratification and Transport (INSTANT) program and satellite-retrieved data (with a horizontal and spatial resolution of 2.5° × 2.5°) indicate that seasonal cycles, particularly those associated with ENSO, significantly impacted surface layer ITF transport during the December to March period, leading to notable reductions in transport between 2014 and 2016 [16]. The ITF volume transport can peak around 14–15 Sv during the southeast monsoon and dip to approximately 10–12 Sv in the northwest monsoon [16].

However, despite its importance, the Halmahera Sea remains one of the least observed ITF routes, with data often limited to indirect modeling and satellite-derived measurements. The complexity of the topography, combined with multiscale interactions—from seasonal monsoons to intraseasonal variability such as the Madden-Julian Oscillation (MJO)—makes this region a dynamic and challenging environment for physical oceanography study [16,17]. As climate change alters the large-scale drivers of ocean circulation, understanding the response and resilience of the Halmahera branch of the ITF becomes increasingly vital.

The primary aim of this review is to synthesize recent findings regarding the role of the Halmahera Sea within the ITF, focusing on its physical mechanisms, climatic modulation, and ecological consequences. Based on the review, we highlight the importance of continued monitoring and research in this region to enhance understanding of the ITF’s broader significance in the Indo-Pacific climate system by compiling observational and modeling studies.

2. The Role of the Halmahera Sea in the Indonesian Throughflow

The Halmahera Sea plays a strategic yet often underrepresented role in the ITF system as an eastern conduit for transferring warm, low-salinity Pacific water to the Indian Ocean [17,18]. Although the Makassar Strait has been recognized as the primary pathway—contributing approximately 77–80% of the total ITF transport [6,19]—the Halmahera Sea and its associated straits, such as the Lifamatola Passage and Molucca Sea, function as complementary routes that contribute significantly to inter-basin water mass exchange. Observational estimates suggest that the Halmahera branch of the ITF transports approximately 1.5 to 2.44 Sv, reinforcing its role in modulating the hydrodynamic and thermal balance across the Indonesian seas [5,12,20].

Geographically, the Halmahera Sea links the western boundary currents of the Pacific Ocean, including the North Equatorial Current and the Mindanao Current, to the internal circulation of the Indonesian seas. This location makes it a key junction for water entering the archipelago from the north and northeast. Water masses in the Halmahera Sea navigate through complex bathymetry and narrow passages before merging with the southward flow through the Banda and Flores Seas, ultimately exiting into the Indian Ocean. The depth and topographic configuration of the Halmahera Sea, including sills and ridges, influence water column stratification and the layering of thermocline waters, affecting the efficiency and properties of inter-ocean exchange [13,21].

Furthermore, the Halmahera route enhances the overall resilience and redundancy of the ITF system by providing an alternate pathway that supports continued transport during disruptions in the primary Makassar route. For instance, seasonal wind reversals or freshwater input from the Java and South China Seas can temporarily reduce transport through the Makassar Strait (Table 1) [19,22]. In such cases, the Halmahera Sea can compensate, maintaining continuity in heat and salt redistribution between ocean basins. This buffering capacity is particularly vital under shifting climate regimes, where increased variability and extreme events such as strong El Niño years can significantly alter dominant oceanic circulation pathways [23,24]. Thus, acknowledging the Halmahera Sea’s role within the broader ITF framework is essential for understanding not only regional oceanography but also global thermohaline circulation and climate feedback mechanisms. Its contribution to multiscale processes—ranging from local upwelling and nutrient cycling to planetary-scale heat transfer—underscores the need for enhanced observational efforts and high-resolution modeling in this dynamically complex region. Moreover, a study using numerical models revealed that tidal mixing within the Halmahera Sea significantly contributes to the transformation of ITF waters, accounting for approximately 76% of mixing events. This process ensures that nutrient-rich waters ascend to the surface, further enhancing local upwelling systems [21].

Table 1. Quantitative estimation of the most important parameters across ocean basins reported in the literature.

Parameter	Description	Quantitative Estimate	References
Transport through Makassar	Average transport rate during normal conditions	~15 Sv	[19]
Seasonal Wind Reversals	Impact on transport rate during reversals	Decrease by ~30%	[22]
Freshwater input	Average freshwater influx from the Java Sea	~500 m3/s	[19]
Halmahera Sea compensation	Increased transport to maintain heat/salt balance	~5 Sv increase	[22]
Heat redistribution	Change in heat content due to transport variations	~1.5 °C fluctuation	[19,22]
Salt redistribution	Change in salinity levels during seasonal events	~0.5 PSU fluctuation	[19,22]

The inflow of Pacific water into the Halmahera Sea is a dynamic process, actively influenced by regional eddies. The New Guinea Coastal Current (NGCC) carries South Pacific water westward, and its path is heavily influenced by the quasi-permanent Halmahera Eddy. This large anticyclonic eddy, located northeast of Halmahera, modulates the volume of water that is steered south into the Halmahera Sea [25,26]. The strength and position of this eddy vary seasonally, thus regulating the volume of water entering this eastern pathway. Concurrently, the retroflection of the Mindanao Current, influenced by the Mindanao Eddy, further dictates the amount of Pacific water available to flow south into the Indonesian archipelago, highlighting a complex interplay of current-eddy interactions at this oceanic gateway [26].

The eddy kinetic energy (EKE) in the region reached approximately 0.1316 m²/s² in 2023 and approximately 0.1341 m²/s² in 2024 (Figure 2). The EKE value showed a significant increase from 2023 (Figure 2a) to 2024 (Figure 2b), reflecting changes in ocean current dynamics that could impact the region’s oceanographic dynamics and consequently the ecosystem.

Figure 2. The spatiotemporal average of Eddy Kinetic Energy (EKE) in 2023 (a) and 2024 (b) in the Halmahera Sea, using data from the Copernicus Marine Service (CMEMS). The black arrow on the map indicates the direction of the NGCC—the direction of the current flows westward. The Halmahera Eddy (HE), located near the island of Halmahera, is a prominent feature on the map, characterized by a circular pattern of high EKE values.

The strategic role of the Halmahera Sea is also fundamentally defined by its bathymetry. The sea is separated from the deeper Pacific Ocean by a prominent submarine ridge with a controlling sill depth of approximately 700 m [20]. This sill is too shallow to allow deeper Pacific water masses, such as the core of the Antarctic Intermediate Water (AAIW), to pass through. Consequently, only the upper and lower thermocline waters of the Pacific can enter the Indonesian Seas via this route, effectively determining the initial properties of the eastern ITF component [12,18]. This passage over a restrictive sill serves as a key site for intense vertical mixing, initiating the transformation of Pacific water properties before reaching the main internal basins of Indonesia and mixing with other water sources.

3. Seasonal and Interannual Variability in the Halmahera Throughflow

The Halmahera Sea, part of the eastern ITF system, shows significant variability across seasonal and interannual timescales, mainly driven by monsoonal wind patterns and large-scale climate phenomena like the ENSO [27]. The quantitative analysis shows that seasonal variability in surface wind forcing causes notable fluctuations in ocean currents and transport within the Halmahera Sea, with average current speeds between 0.1 and 0.5 m/s across different seasons. In boreal winter (December–February), the prevailing northeast monsoon boosts surface water convergence toward the southern Philippine Sea, enhancing transport into the Halmahera Sea through the Mindanao Current and North Equatorial Current branches [13,24]. Conversely, the southwest monsoon in boreal summer (June–August) weakens this inflow and frequently redirects surface currents northward, diminishing the strength of southward ITF transport through the Halmahera region, with a recorded transport volume decrease of about 20–30% compared to winter months.

The Indonesian seas serve as a crucial oceanic route for interactions between interannual variations in the Pacific and Indian Oceans, including signals from the ENSO and the Indian Ocean Dipole (IOD) that modulate the effect of the MJO. Within the ocean, the IOD can influence the Pacific Ocean through the transmission of Indian Ocean Kelvin waves across the Indonesian Seas [28]. ENSO is one of the most significant interannual factors influencing Halmahera throughflow dynamics. During El Niño events, the average reduction in volume transport through the Halmahera Sea can reach up to 50%, as weakened easterly trade winds lead to a shoaling of the thermocline and a decrease in sea level in the western Pacific, thereby suppressing the pressure gradient that drives the ITF. This results in reduced volume and cooler, less saline water entering the Halmahera Sea [22,29]. Conversely, La Niña events strengthen the ITF by intensifying trade winds and deepening the Pacific thermocline, thereby increasing the inflow of warm, nutrient-rich water masses through Halmahera and adjacent straits, with transport volumes potentially increasing by 30–40% during these periods [14,30]. These variations lead to seasonal changes in thermal structure and salinity, directly impacting water mass transformation and ocean-atmosphere heat exchange in the region.

As demonstrated in the study by [31], the interannual variability of local winds and the ITF in the Makassar Strait and Halmahera Sea was investigated. In their analysis, current velocities at consistent grid points were used to represent the simulated ITF in both regions. The results of the quantitative assessments reveal that the interannual variability of local winds and currents in the Makassar Strait and Halmahera Sea, after removing climatological seasonal cycles from 2000 to 2016, shows significant anomalies, with average wind speeds fluctuating between 5 and 10 m/s. These variations lead the Niño 3.4 index by approximately 3–4 months—northward during El Niño and southward during La Niña. Velocity profiles in both straits exhibit opposite vertical anomalies: in Makassar, surface currents generally align with local winds except during 2006–2007, 2012–2013, and mid-2016, while in Halmahera, surface currents tend to oppose local winds during ENSO events. The model captures southward (El Niño) and northward (La Niña) anomalies in the upper 100 m of Makassar, with reversed patterns between 100–700 m, including a notable velocity decline in summer 2016 (horizontal and temporal resolution of 0.25° × 0.25°) [32] and sub-thermocline strengthening in 2008 and 2016 [19,33]. To assess the model skill, various statistical metrics were employed, including correlation coefficients, which indicated a high correlation (r > 0.7) between observed and simulated transport, demonstrating its reliability in capturing the dynamics of the Halmahera Throughflow [32]. In Halmahera, autonomous surface vehicles show northward anomalies at 0–200 m and southward at 200–700 m during El Niño, with reversed patterns during La Niña. Furthermore, the observed subsurface anomalies precede surface signals and local winds by 2–3 months, indicating a clear temporal relationship that suggests remote ENSO-driven forcing via Pacific-origin Kelvin and Rossby waves [31].

In addition to ENSO, intraseasonal oscillations such as the MJO further modulate short-term variability in the Halmahera Sea by altering atmospheric convection, wind stress, and precipitation patterns. Ref. [16] observed that MJO activity affects surface-layer transport through the Makassar Strait, and similar mechanisms are expected to influence flow through Halmahera. Moreover, variations in freshwater input from the South China Sea and Java Sea—especially during extreme monsoon years—can interact with background ITF flows, forming a “freshwater plug” that alters stratification and suppresses deep water exchange, with impacts measurable in terms of salinity gradients of up to 2 PSU [19,34]. These combined seasonal and interannual signals result in complex, non-linear flow behavior in the Halmahera Throughflow, with important implications for ocean mixing, heat storage, and regional climate feedback.

Given the sensitivity of the Halmahera Throughflow to both internal ocean dynamics and external climate forcing, sustained observations and high-resolution modeling are essential to capture its variability accurately. Understanding these changes is critical for predicting downstream impacts on the Banda and Indian Oceans, as well as for anticipating future alterations under climate change scenarios.

4. Mixing and Connectivity in the Halmahera Sea

Oceanographic conditions in the Halmahera Sea are also affected by tidal dynamics and the presence of sea sills, which act as thresholds influencing current behavior [35,36]. The region’s complex topography causes significant changes in current patterns, particularly in terms of velocity and direction. For instance, during tidal cycles, current speeds can fluctuate by up to 0.2 m/s, leading to alterations in the transport of water masses across the region [13]. The ITF flows through the Halmahera Sea, with a width of 67.2 km and a depth reaching 700 m. It features two main core layers at depths of 100 m and 400 m [13]. In the upper layer (up to 100 m), the flow velocity can exceed 0.4 m/s, which is higher than the velocity in the layer below the thermocline.

Tide-induced mixing is particularly important in the Halmahera Sea due to the region’s intricate seafloor topography, characterized by deep basins and sills that enhance turbulent dissipation. Observations from the INDOMIX campaign indicated strong vertical energy dissipation in the Halmahera Sea, especially around constricted straits and ridges, suggesting active diapycnal mixing that facilitates the vertical redistribution of heat and salt [21]. In addition, internal tides and internal waves generated by topographic interactions contribute to the transformation of water masses by increasing the vertical flux of momentum and tracers, which ultimately influences the thermocline structure downstream [10].

Mesoscale eddies and gyre interactions also play an influential role in shaping Halmahera throughflow characteristics. Studies have shown that eddies originating from the Pacific or formed within the Indonesian seas can interact with boundary currents such as the Mindanao and Halmahera Currents, leading to lateral mixing and variability in flow pathways [33]. These eddy-mean flow interactions can entrain distinct water masses or divert flow through alternate routes, thus enhancing water property diversity within the Halmahera Sea. Furthermore, interactions between the ITF and inflows from the South China Sea—especially during monsoonal reversal—can alter halocline structures and reinforce water mass transformations, as the convergence of different salinity layers promotes enhanced mixing [29,34].

The Halmahera Sea is characterized as relatively shallow water compared to the surrounding waters. A portion of the water is from the Southern Pacific Ocean, which has different temperature and salinity profiles than those from the Northern Pacific Ocean, and it is often influenced by mesoscale eddies and gyres. The mixing of these waters in the shallow Halmahera Sea region, as well as the increasing mixing when they flow downstream to the Banda Sea, has attracted growing research attention.

Seasonal variability in the Halmahera Sea primarily results from monsoonal wind patterns. During the northeast monsoon, currents are enhanced, leading to increased transport into the Halmahera Sea. Conversely, during the southwest monsoon (June to August), the reduced inflow can diminish nutrient availability, leading to less phytoplankton growth and shifting marine ecosystems (Table 2) [15,37]. Interannual changes linked to ENSO are particularly impactful. Quantitative studies indicate that during El Niño years, ITF transport can decrease significantly, leading to observable impacts on regional ocean temperatures and salinity profiles. The La Niña phase can reverse this, increasing transport significantly as stronger trade winds enhance the inflow of warmer waters, affecting local biological productivity and thermal stratification in the Halmahera Sea (Table 2) [8].

Table 2. Key influencing factors on Halmahera currents.

Impact Factor	Description	References
Seasonal monsoons	The northeast monsoon strengthens transport into Halmahera, while the southwest monsoon weakens it, causing significant current fluctuations	[12,15]
ENSO events	El Niño diminishes ITF flow, reducing volume from the Pacific, while La Niña enhances flow, increasing the influx of warm waters	[8,15]
Tidal dynamics	Tides induce significant mixing and alteration of water mass characteristics, particularly in deeper layers of the Halmahera Sea	[4,37]
Freshwater inputs	Variations in freshwater influx from surrounding seas can disrupt stratification and influence mixing processes in the Halmahera Sea	[38]
Interannual climate variability	Changes in atmospheric conditions affect ocean temperature and salinity, impacting current patterns and regional climate feedback	[4,7,39]

The dynamics of the Halmahera Sea significantly influence the Indonesian seas and connect to broader Pacific and Indian Ocean systems. The ITF, through the Halmahera passage, serves as a channel for heat and energy transfer across basins [4]. This connectivity is evidenced by the propagation of climate signals, where changes in sea surface temperature in the Indian Ocean can impact ENSO developments through variations in ITF [8,39]. Moreover, enhanced ITF flows can influence cold anomalies from the eastern Pacific back to the Indian Ocean, suggesting a reciprocal relationship with larger climate patterns [8,39].

Overall, the Halmahera Sea is central to a complex system of oceanic conveyance influencing broader climatic processes. The Halmahera Sea is unique for its relatively shallow depth and its connection to water from the Southern Pacific Ocean. These interconnections highlight the imperative to understand and quantify the interactions within this region, emphasizing the need for ongoing observation and modeling to predict future climate variability and its potential impacts on marine and atmospheric systems.

5. Ecological and Climatic Implications of Halmahera Throughflow Dynamics

The dynamic nature of the ITF through the Halmahera Sea carries significant implications for both regional marine ecosystems and broader climate systems. As a minor yet critical pathway for the ITF, the Halmahera Sea facilitates the movement of warm, low-salinity waters from the western Pacific into the Banda and Indian Oceans. This continuous water transport influences thermohaline circulation and regional heat distribution while supporting nutrient cycling, primary productivity, and biodiversity in the Indonesian seas [40,41]. Variability in the flow—driven by climatic factors such as ENSO and monsoonal winds—can trigger fluctuations in nutrient upwelling, chlorophyll-a concentrations, and biological productivity, ultimately impacting fish stocks and food webs in surrounding regions.

Reference [38] highlights a strategically important region in Southeast Asia and the western Pacific, encompassing countries such as Malaysia, Singapore, Brunei Darussalam, the Philippines, Timor-Leste, and Australia. These locations lie adjacent to the pathway of the Halmahera Throughflow, which plays a critical role in redistributing water masses, heat, and nutrients between the Pacific and Indian Oceans. The dynamics of this current significantly influence regional ecological conditions, including marine biodiversity, productivity, and coral reef health, while also impacting local climate patterns such as seasonal rainfall variability and the frequency of extreme events (e.g., El Niño). Furthermore, the interaction between this throughflow and the complex seafloor topography around Halmahera can generate nutrient-rich upwelling zones, though it may also alter plankton communities and fish species dependent on stable temperature and salinity conditions. Understanding this current system is crucial for predicting climate change effects and ensuring sustainable marine resource management in the Indo-Pacific region.

Changes in Halmahera Throughflow strength and structure also affect sea surface temperatures (SSTs), which in turn modulate atmospheric convection and precipitation patterns over the Indo-Pacific. During La Niña phases, stronger ITF transport through Halmahera enhances the export of warm water to the Indian Ocean, contributing to increased SST anomalies and altered monsoon intensity in Southeast Asia [14,30]. Conversely, during El Niño events, weakened throughflow reduces ocean heat transport, potentially leading to suppressed rainfall over the maritime continent and disrupted climatic equilibrium [42]. These ocean-atmosphere feedback mechanisms highlight the role of the Halmahera Sea not just as a physical conduit but as a critical player in modulating regional hydroclimate patterns. These SST processes also impact local ecosystems.

Ecologically, the Halmahera Throughflow contributes to shaping genetic connectivity and species distributions in eastern Indonesia. Variability in current strength and direction can either enhance or impede larval dispersal and gene flow among marine populations. For instance, studies on crustacean species suggest that ITF dynamics modulated by features such as the Mindanao Eddy and Halmahera eddies act as both physical barriers and facilitators for population mixing. Furthermore, the inflow of nutrient-rich Pacific waters supports high primary productivity in downstream ecosystems, which is essential for sustaining coral reef communities, pelagic fisheries, and benthic habitats in the Banda and Arafura Seas [5,41]. Disruptions to the throughflow caused by climate change or anthropogenic factors could, therefore, have cascading effects on ecosystem structure, fisheries productivity, and coastal resilience.

Considering these implications, monitoring the Halmahera Throughflow becomes a priority for oceanographic understanding and marine conservation, and climate adaptation strategies. Integrating satellite remote sensing, in situ measurements, and ecological modeling will be essential for quantifying the ecological thresholds and climatic tipping points associated with flow variability in this region.

In situ measurements conducted in the area reveal notable variations in both salinity and temperature, with salinity ranging from 34.4 to 34.8 PSU and temperatures fluctuating between 15 °C and 20 °C. These changes indicate the presence of a thermocline at depths of 100–200 m (Figure 3). At the same time, nutrient concentrations tend to increase with depth, reaching approximately 3–5 mmol/m³ at depths between 70 and 150 m (Figure 3). These trends align with the temperature/salinity profile, suggesting that this layer is rich in nutrients, primarily due to organic matter decomposition and upwelling from the seabed [19].

Figure 3. T-S and nutrient profile at longitude 128°58′59.95″ E and latitude 1°27′40.33″ N (Halmahera Sea) with the station on the map as a yellow dot, using Conductivity Temperature Depth (CTD) data from the Ministry of Marine and Fisheries Affairs (MMAF) fish stock assessment in Fisheries Management Area (FMAs 711) on 17 June 2015.

The T-S profile shows a rapid decrease from around 30 °C at the surface to approximately 10 °C at a depth of 200 m (Figure 4). This indicates the presence of a strong thermocline layer at a depth of around 100–150 m. Similarly, the salinity profile exhibits a significant change within the same depth range as the thermocline, suggesting the existence of a halocline (sharp change in salinity) at these depths (Figure 4). The vertical patterns of temperature and salinity changes demonstrate that the depth and topographic configuration of the Halmahera Sea play an important role in shaping the water column stratification and the distribution of thermocline waters in this region.

Figure 4. T-S profile at station (shown in Figure 3) using data from the Copernicus Marine Service (CMEMS) and the Coastal and Regional Ocean Community Model (CROCO Model) with a resolution of 1/12° on 17 June 2015.

In general, the model results are able to describe the vertical patterns of temperature and salinity effectively, in accordance with the results of measurements at various depths. The temperature results at a depth of 50 m with the CROCO model showed a value of 28 °C, while the CMEMS model showed 29 °C. Both of these values are slightly lower than the measured results, which reached 30 °C. The salinity results at a depth of 50 m: the CROCO model showed a value of 35.2 PSU, while the CMEMS model showed 35.3 PSU. Both of these values are quite close to the measured results, which reached 35.4 PSU. In general, the CROCO and CMEMS models are effective in describing the vertical patterns of temperature and salinity, although there is a small difference in the absolute value of the temperature at a depth of 50 m compared to the measured results. However, these models are representative in describing the actual conditions in the Halmahera Sea.

6. Extreme Events on the Halmahera Throughflow

In recent decades, extreme events such as pronounced anomalies in sea surface temperature, changes in monsoon winds, and the dynamics of phenomena like the ENSO and the IOD have significantly affected the behavior of the current through the Halmahera Sea. One notable event occurred in 2016, when the ITF weakened by 25–38% from an average transport value of approximately −2.6 Sv to around −1.6 to −1.95 Sv due to a negative IOD anomaly [16]. This weakening specifically applies to the Halmahera branch of the ITF and represents a significant deviation from typical seasonal transport patterns, highlighting the impact of interannual climate variability on regional ocean dynamics [16]. This weakening was driven by an increase in sea surface height and temperature along the coasts south of Sumatra and Java, which reduced the pressure gradient between the Pacific and Indian Oceans [40]. As these gradients decreased, the volume of water transported by the ITF, including the Halmahera Sea branch, diminished considerably. This situation was further exacerbated by the strengthening of westerly winds (Wyrtki jets) and the propagation of downwelling Kelvin waves in the Indian Ocean, both triggered by negative IOD conditions [16].

The influence of ENSO, particularly during strong La Niña events, also plays an important role. Studies have shown that Rossby waves originating from the tropical Pacific can influence water flow patterns in both the Makassar Strait (the western route) and the Halmahera Sea (the eastern route), affecting water mass transport at different depths [31]. Specifically, the Halmahera route receives ENSO signals through barotropic wave propagation, reflecting nonlinear conditions in the Sulawesi Sea [43,44]. Satellite data, including altimetry and gravimetry, have been instrumental in monitoring long-term fluctuations in ITF transport volume. Research indicates that seasonal and interannual variability can be traced by differences in sea surface pressure at key locations such as 162° E and 11° N in the Pacific and 80° E in the Indian Ocean [45]. This highlights the role of the Halmahera Sea as an adaptive pathway that responds to spatial pressure differences between the oceans. Furthermore, the region experiences strong tidal mixing, which plays a crucial role in redistributing energy and nutrients, thereby impacting the thermohaline dynamics locally. These mixing processes influence water mass stratification and modulate the region’s response to climatic anomalies. Data from the INSTANT (International Nusantara Stratification and Transport) program demonstrate that the variability of the current along the ITF routes, including the Halmahera branch, is heavily influenced by seasonal wind patterns, pressure conditions, and extreme climate events such as El Niño in 1997 and La Niña in 2007 [6].

7. Conclusions

The Halmahera Sea plays a pivotal yet often underappreciated role within the ITF system, serving as a critical conduit for the transfer and mixing of warm, low-salinity waters from the Pacific Ocean to the Indian Ocean. This review highlights the complex dynamics governing the Halmahera Sea, emphasizing its significance in modulating regional oceanography and climate. The ITF is not merely a singular current; it is a network of interconnected straits and seas, with the Halmahera Sea contributing significantly to the overall water for tidal mixing through its typical temperature and salinity characteristics. Seasonal and interannual variability, particularly influenced by monsoonal winds and large-scale climate phenomena, such as the El Niño-Southern Oscillation, greatly impacts flow dynamics in this region. These fluctuations affect not only the volume and direction of water transport but also the thermohaline structure, which is crucial for nutrient cycling and marine biodiversity. The interplay of various oceanographic processes, including vertical mixing and mesoscale eddy interactions, further enhances the complexity of water mass transformations in the Halmahera Sea. Given the increasing pressures of climate change and anthropogenic influences, understanding the Halmahera Sea’s role in the ITF is essential for predicting future shifts in ocean circulation and climate patterns. Enhanced observational efforts and high-resolution modeling are necessary to capture the nuances of this dynamic region. Ultimately, recognizing the Halmahera Sea’s contributions to global thermohaline circulation and its ecological implications is vital for effective marine resource management and climate adaptation strategies in the Indo-Pacific region.