Wetland ecosystems are vital for both biodiversity and communities that depend on them. The Ligawasan Marsh in the Southern Philippines is one of the most threatened wetlands in the country. Apart from growing anthropogenic developments (e.g. natural gas extraction and industrialisation), marshes face warfare-driven threats that have hindered research and conservation efforts in the area for many decades. Our study is the first to investigate the patterns of physicochemical parameters, the impact of land-use changes on the environmental status of the marshland, and the contribution of surrounding towns. We found a strong negative correlation between dissolved oxygen (DO) and indicators of pollution such as biochemical oxygen demand (BOD), chemical oxygen demand (COD), and heavy metals. Interestingly, we observed elevated levels of phosphate and mercury at all sampling sites within the Ligawasan Marsh. Our landscape-level modelling showed that these elevated levels are associated with expanding croplands and urbanisation. Furthermore, we utilised our newly developed Marshland Impact Area (MARia) Index. We found that the potential impact contribution of cropland and urbanisation from surrounding towns of the Ligawasan Marsh varied significantly, suggesting the importance of implementing local policies to reduce land use change impacts. With the current limited knowledge and beyond safe pollution levels in the Ligawasan Marsh, it is crucial to implement collaborative and science-based governance to integrate conservation initiatives with the priorities of global targets, such as the Kunming-Montreal Global Biodiversity Framework, for a comprehensive and sustainable approach to Ligawasan Marsh conservation.