Coastal tropical waters are experiencing rapid increases in anthropogenic pressures, yet coastal biogeochemical dynamics in the tropics are poorly studied. We present a multi-year biogeochemical time series from the Singapore Strait in Southeast Asia’s Sunda Shelf Sea. Despite being highly urbanised and a major shipping port, the strait harbours numerous biologically diverse habitats, and is a valuable system for understanding how tropical marine ecosystems respond to anthropogenic pressures. Our results show strong seasonality driven by the semi-annual reversal of ocean currents: dissolved inorganic nitrogen (DIN) and phosphorus varied from ≤0.05 µmol l-1 during the intermonsoons to ≥4 µmol l-1 and ≥0.25 µmol l-1, respectively, during the southwest monsoon. Si(OH)4 exceeded DIN year-round. Based on nutrient concentrations, their relationships to salinity and coloured dissolved organic matter, and the isotopic composition of NOx-, we infer that terrestrial input from peatlands is the main nutrient source. This input delivered dissolved organic carbon (DOC) and nitrogen, but was notably depleted in dissolved organic phosphorus. In contrast, particulate organic matter showed little seasonality, and the δ13C of particulate organic carbon (-21.0 ± 1.5‰) is consistent with a primarily autochthonous origin. Diel changes in dissolved O2 varied seasonally with a pattern that suggests that light availability controls primary productivity more than nutrient concentrations. However, diel changes in pH were greater during the southwest monsoon, when remineralisation of terrestrial DOC lowers the seawater buffer capacity. We conclude that terrestrial input results in mesotrophic conditions, and that the strait might be vulnerable to further eutrophication if nutrient inputs increase during seasons when light availability is high. Moreover, the seasonality of diel pH variation suggests that coral reefs exposed to terrestrial organic matter in the Sunda Shelf may be at significant risk from future ocean acidification.