A 3D multilevel eutrophication model has been developed and applied to the tropical coastal waters of Singapore. The model considers the nitrogen, phosphor-us, and carbon cycles; phytoplankton and zooplankton dynamics; and dissolved oxygen balance in the water column coupled to benthic processes and is driven by a 3D multilevel hydrodynamic model. The eutrophication model was calibrated with field data obtained from the Southwest Monsoon in August 1998 and subsequently validated using data from the Northeast Monsoon in December 1998. Predictions of nutrient and phytoplankton concentrations from the model simulation agreed well with the observed data. The model results show that the coastal waters of Singapore are relatively well-mixed and differences in concentration with depth for all state variables are generally < 20%. In the Singapore Strait, horizontal spatial differences for all the variables are generally < 40%. In the Southwest Monsoon, slightly larger values for phytoplankton and dissolved oxygen but smaller nutrient values are found in the eastern region of Singapore, compared to the west. The reverse trend is found in the Northeast Monsoon.