Across the 62,146 ha surveyed, this study found 15,320 ha of combined seagrass meadows, bivalve beds, and corals along the coastline of southeastern Cambodia (Figure 1). Specifically, this study identified 11,569 ha of seagrass, 2,688 ha of bivalves, and 1,063 ha of coral throughout the four survey zones. Kampot had the highest overall habitat cover and percent coverage per area surveyed (Table 1). Koh Seh exhibited the least overall habitat presence. Bivalve presence was the highest in Kampot with 1,238 ha (5.09% coverage), followed by 1,153 ha (4.55% coverage) in Outer Kep, 297ha (2.66% coverage) within Kep MFMA, and 0ha in Koh Seh. Coral had the lowest observed coverage overall and was the most abundant in Kampot, covering 861ha (3.54% coverage), followed by 59ha in Koh Seh (4.46% coverage), 68ha within the Kep MFMA (0.61% coverage), and 75ha in Outer Kep (0.29% coverage). The greatest seagrass extent was observed at 5,158 ha in Kampot (21.32% coverage), followed by 3,642 ha (14.38% coverage) in Outer Kep, 2,757 ha (24.69% coverage) within the Kep MFMA, and 12ha around Koh Seh (0.91% coverage) (Table 1).

There was remarkably high seagrass diversity, with 10 species recorded during the surveys and up to six species observed in one free-dive (Table 2). The greatest species richness was found in Kampot with 10 species, but the greatest Shannon–Weiner Diversity was observed within the Kep MFMA (H′ = 1.60), followed closely by Kampot (H′ = 1.55) and then Outer Kep (H′ = 1.25). Koh Seh had only one species present, Thalassia hemprichii (H′ = 0, α = 1). Kampot, Outer Kep, and Kep MFMA had high alpha diversities of α = 10, α = 9, and α = 9, respectively.

Seagrass, corals, and bivalves were recorded at mean depths of 2.7, 3.9, and 3.7m, respectively, and at maximum depths of 6.9, 6.5, and 11.0m, respectively. The average depth of the entire survey area was 4.4m. Sediment analysis revealed that benthic habitats were primarily found in areas with coarse and fine sand, with less habitat cover observed in muddy substrates (Figure 2).

The GAMs revealed significant influences on habitat presence (Figure 2). The GAMs explained 86.9%, 60.4%, and 56.7% of the deviance for seagrass, bivalve, and coral presence, respectively. Muddy substrate has a negative effect on seagrass presence compared to both coarse substrate (p = 0.006) and fine substrate (p = 0.008). Substrate type had no other significant effects on habitat presence (p > 0.05). The interaction between the effects of mud and depth on seagrass presence was marginally significant (p = 0.049), indicating that the negative effect of mud varied with depth. Depth had a negative relationship with seagrass, bivalves, and coral (p = 1.08e−10, p = 0.0004, and p = 0.02, respectively). The spatial smooth term was significant for all habitat type models, indicating that all habitat distributions were influenced by spatial factors.

Residual plots showed most of the binned residuals sitting within the 95% confidence interval with no clear pattern. This indicates that there is a good model fit with no bias and little heteroscedasticity. A histogram of the residuals shows a high kurtosis, which is expected for binary data since the residuals are constrained to a limited range. This indicates that most predictions are close to the observed values, with some spread in the tails likely linked to spatial outliers. The residuals of the GAMs did not exhibit spatial autocorrelation (Moran’s I statistic = −0.0002, p = 0.5); however, by splitting the entire region into sufficiently small areas, some of those areas generated a Moran’s I p < 0.05, indicating that some smaller-scale spatial autocorrelation remains. Multicollinearity was assessed using VIF, of which each variable had a value < 3, indicating some moderate correlation but no problem of collinearity.

The pioneer species Halophila spp. were observed in abundance in close proximity to FPSs, indicating regrowth in areas now protected from trawlers.

Documenting the success of FPSs in Cambodia is important so that other countries with high levels of subsistence fishing may also benefit. FPSs have been positively received by small-scale fishermen and villages in Cambodia; however, these conservation measures have been underutilized as a way to combat illegal, unregulated, and unreported (IUU) trawlers in other parts of the world. FPSs present an opportunity for blue economies with limited resources for Marine Protected Area (MPA) enforcement. Cambodia will serve as a case study of the benefits that these passive marine protections can bring to the livelihoods of fishermen who have struggled with the ecological impacts of rampant IUU activities and suggests that habitat protections provided by FPSs can form the basis of a regionally scalable solution to illegal fishing within the blue economy framework.

Depth is a key driver with a strong negative effect on benthic habitats, which can most likely be explained by reduced light availability from the region’s high turbidity and increased trawler accessibility, as local trawlers can only operate in deeper waters. Outside of areas protected by FPSs, seagrass was only found in shallow nearshore areas. For instance, the regions of the Kampot and Outer Kep survey zones exhibited their highest seagrass concentrations in shallow waters naturally restricted to trawling vessels (Figures 1, 2), while Kep MFMA exhibited seagrass meadows at greater depths, suggesting that protections offered by the MFMA allow for benthic habitat recovery beyond the shallow zone. In our study, seagrass meadows were generally concentrated in shallow areas less accessible to trawling gear. The shallow depth profile is expected for T. hemprichii and Enhalus acoroides; however, this was particularly surprising for Halophila spp. and Halodule spp., which have been commonly recorded at 20m or deeper in other Southeast Asian countries (Green and Short, 2003; Duarte, 1991). In this study, Halophila spp. were recorded with maximum depths reaching 6.90 m in the Kep MFMA and 3.87 m on average. Halodule spp. were observed at depths of up to 4.00m, averaging 2.51m. These patterns are most likely due to persistent bottom trawling at greater depths. The comparatively low habitat presence in Koh Seh likely reflects both deeper bathymetry and greater trawling accessibility. In contrast, Kampot benefits from extensive shallow areas that restrict trawling vessels, supporting higher seagrass and coral cover.

Our observations suggest that bottom trawling activity is a strong determinant of benthic habitat presence in the region, as seagrass was primarily located in areas too shallow for trawling to occur, except in the MFMA, where FPSs reduce trawling activity. These findings underscore the importance of integrating FPSs into marine spatial planning efforts, aligning with blue economy goals of sustainable resource management. The average depths of seagrass in Kampot, Outer Kep, and Kep MFMA were 2.02, 2.56, and 3.41m, respectively, indicating that seagrass can grow in deeper areas with FPS protections. This is in agreement with a report by the Cambodian Department of Fisheries, which found that overfishing and destructive fishing are among the highest risks to benthic habitats in the region (Sitha, 2005; Fisheries Administration, 2020). However, future studies should quantify trawling activity in the region in order to further support this claim.

Mud had a significantly negative relationship with seagrass presence compared to fine and coarse sediment, which may be explained by higher turbidity interfering with light availability (Zabarte-Maeztu et al., 2021). Substrate type had no significant effect (p > 0.05) on coral or bivalve presence, despite the differences seen in Figure 2. The spatial smooth term revealed significant localized variability, which would be indicative of unmeasured effects such as trawler activity, water quality, or other unobserved processes.

The Indo-Pacific contains the greatest seagrass species diversity on the planet, with up to 14 distinct species inhabiting a single reef flat (Short et al., 2007). This study found 10 species across the four survey zones, with prior studies finding 10–11 species in the same region, constituting one of the highest species richness globally (Table 2) (Leng et al., 2014; Ouk et al., 2010; Supkong and Bourne, 2014; Coles et al., 2011). The Kep MFMA had the highest Shannon–Weiner Diversity, suggesting that the additional fishing protections, FPSs, and patrolling occurring in the MFMA are aiding conservation. Despite the high species richness, only two species dominate across the region—E. acoroides and T. hemprichii—both of which have been found to have increased tolerance for high sedimentation rates (Terrados et al., 1998).

Due to budget constraints, this study largely relied on a free-diving systematic GPI survey, which assumes that each point is representative of a 250-m² area. Despite the lower resolution, this study’s large sample size achieved wide-scale data, thus still providing an adequate estimate of benthic habitat presence. Additionally, the authors recognize that a change in the benthic composition may have occurred during the pause in surveying over the rainy season, as well as throughout the active surveying periods, due to ongoing bottom trawling. Nevertheless, this study provides the most recent data for the region.

To improve scalability, future surveys could combine GPI with remote sensing, drones, or acoustic methods to efficiently cover larger areas while retaining ground-truthing detail. Conserving essential fish habitat is a critical step to protect and prolong sustainable blue economies. Future studies should assess changes in the region’s fish biomass to better examine the socioeconomic impacts of FPSs (Floyd et al., 2024). Long-term monitoring is also essential to track changes in habitat coverage over time, especially in response to the deployment of FPSs and the designation of MFMAs.

While this study offers a valuable baseline for future conservation efforts, it also underscores the urgency of addressing illegal fishing practices to preserve the remaining benthic habitats in Cambodia’s coastal waters. Beyond biodiversity and fisheries values, seagrasses are globally significant blue carbon sinks, with potential to mitigate CO₂ emissions and contribute to national climate goals (Fourqurean et al., 2012). Their combined role in carbon storage, biodiversity support, and food security means that their decline has broader implications for socioeconomic stability in coastal communities. Protecting and restoring these ecosystems could help Cambodia, and potentially many more countries, to meet their carbon-neutral goals while supporting local fisheries and coastal protection (UNFCCC, 2021). These insights are particularly relevant for other Southeast Asian nations facing similar marine governance challenges, offering a model for inclusive and low-cost blue economy interventions (Strain et al., 2018). In practical terms, the most effective management strategies emerging from this work are i) continued deployment of FPSs to passively deter illegal trawling, ii) strengthening of MFMA enforcement and patrols, and iii) integration of community-led monitoring into management. Together, these strategies offer a replicable framework for coastal nations with limited enforcement capacity.

In Southeast Asia, there is both an outsized need for the ecosystem services that benthic habitats provide and a marked absence of data (Kirkman and Kirkman, 2002; Boon et al., 2014; Voe et al., 2015). This study provides the first comprehensive assessment of benthic habitats in southeastern Cambodia, offering necessary data for future conservation efforts. The results indicate that illegal trawling remains the primary threat to seagrass meadows, corals, and bivalve beds in the region. This not only impairs biodiversity but also jeopardizes the long-term viability of Cambodia’s blue economy, where sustainable fisheries, tourism, and coastal livelihoods are dependent on healthy marine ecosystems. Fortunately, the continued patrolling, advocacy for protected area delineation, and deployment of FPSs by MCC will allow the region to begin to recover. The local communities in Cambodia, whose subsistence fishing is directly threatened by illegal bottom trawling, have supported MCC with their grassroots endeavors, backing MPAs and assisting in FPS construction (Hamilton, 2012; Cockerell et al., 2016). This shows promise for the uptake of FPSs by coastal communities around Southeast Asia. Governments around the globe should continue to designate, and soon enforce, MPAs and anti-trawling policies, to ensure not only longevity of the ecosystem but also food security and ecosystem services for the people of coastal Cambodia (Unsworth and Cullen-Unsworth, 2010; Boon et al., 2014). These findings demonstrate that bottom-up marine conservation strategies like FPSs can support biodiversity and fisheries simultaneously, offering a practical pathway toward strengthening a blue economy in Cambodia and beyond.