Understanding how climatic variability impacts coastal water quality is increasingly urgent, but in many regions we lack multi-year, coastal biogeochemical time series that can provide these insights. We analyzed a 7–9-year time series of salinity, dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) from a site in the centre of Southeast Asia’s Sunda Shelf Sea, the Singapore Strait, to understand the biogeochemical variability and corresponding climatic drivers. Our site receives substantial terrestrial inputs via rivers, especially from regional peatlands, but is also subject to seasonal reversal in ocean circulation due to the Asian monsoon system, delivering different water masses in different seasons. We therefore additionally performed realistic hindcast simulations with a regional physical circulation model to understand the impact of physical oceanography. We show that salinity, DOC, and CDOM at our site are significantly correlated with regional precipitation, seawater volume transport, and the climate phenomena El Niño–Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD), both at seasonal and interannual time scales. The impacts of ENSO and IOD appear to result partly from their influence over regional precipitation, but also from direct effects on regional physical circulation. Our results illustrate how physical oceanographic variability can interact with climatic variability to drive coastal biogeochemistry. This highlights the importance of accurately representing such drivers in models for future projections of coastal water quality.