Abstract. Atmospheric deposition of nutrients (N and P species) can intensify anthropogenic eutrophication of coastal waters. It was found that the atmospheric wet and dry depositions of nutrients was remarkable in the Southeast Asian region during the course of smoke haze events, as discussed in a companion paper on field observations (Sundarambal et al., 2010b). The importance of atmospheric deposition of nutrients in terms of their biological responses in the coastal waters of the Singapore region was investigated during hazy days in relation to non-hazy days. The influence of atmospherically-derived, bio-available nutrients (both inorganic and organic nitrogen and phosphorus species) on the coastal water quality between hazy and non-hazy days was studied. A numerical modeling approach was employed to provide qualitative and quantitative understanding of the relative importance of atmospheric and ocean nutrient fluxes in this region. A 3-D eutrophication model, NEUTRO, was used with enhanced features to simulate the spatial distribution and temporal variations of nutrients, plankton and dissolved oxygen due to atmospheric nutrient loadings. The percentage increase of the concentration of coastal water nutrients relative to the baseline due to atmospheric deposition was estimated between hazy and non-hazy days. Model computations showed that atmospheric deposition fluxes of nutrients might account for up to 17 to 88% and 4 to 24% of total mass of nitrite + nitrate-nitrogen in the water column, during hazy days and non-hazy days, respectively. The results obtained from the modeling study could be used for a better understanding of the energy flow in the coastal zone system, exploring various possible scenarios concerning the atmospheric deposition of nutrients onto the coastal zone and studying their impacts on water quality.