The sensitivity of the 3‑D biogeochemical model SPBEM-2 to the inclusion of dissolved organic nitrogen and phosphorus input with river runoff as variables in the model equations was analyzed. The inclusion of the phosphorus and nitrogen loads brought with labile dissolved organic matter (DOM) in the river runoff into the calculations noticeably influences the spatial distribution of the nitrogen and phosphorus sedimentation flux, name ly, leads to an increase in the sedimentation flux in estuarine areas. The sedimentation of detrital nitrogen and phosphorus to the bottom increases 2.5 and 3 times, respectively. The amount of primary production decreases versus the overestimated values in the calculations without DOM equations for the eastern part of the Gulf of Finland. The inclusion of variables describing DOM transformations into the model equations helps avoid the artificial overestimation of the detritus sedimentation rate and use in the model values comparable to the observed ones.