Seagrass bed has an important role in the marine ecosystem of estuarine areas. To conserve and manage these seagrass beds, understanding the system and the role of seagrass is necessary. A three-dimensional physical-biological coupled model (MK-3) was modified to include a seagrass bed and it was applied to Akkeshi lake, on the Pacific coast of Hokkaido in the northern part of Japan. Nitrogen and phosphorus fluxes were evaluated to investigate the role of seagrass on the nutrient cycle. First, a simple box model was developed. We divided the lake into three boxes to estimate the characteristics of the nutrient cycle from observed data. The box model revealed that nitrate is supplied to the lake through physical processes, i.e. river discharge and advection from outer regions and is consumed biologically inside the lake. On the other hand: phosphate is supplied from inside the lake and flows out. Second, to explain this different behavior of nitrate and phosphate, the three-dimensional physical-biological coupled model was applied. The model was run under average meteorological conditions of April for IO days, then a calculation was continued using actual conditions (wind, precipitation, etc.) during 16-27 April 1996. The calculation was carried out for two cases: (I) with eelgrass; and (2) without eelgrass. In the case without eelgrass, nitrate and phosphate were both reduced by biological and chemical processes inside the lake. In the case with eelgrass, nitrate was reduced, but phosphate was produced inside the lake, which was estimated by the box model. Furthermore, the eelgrass was more important than phytoplankton to produce particulate organic matter. The daily variation in chlorophyll a and nitrate, which was observed during 16-27 April 1996, could not be reproduced in the model results, although the average values coincided with the observed values. This may be because of the effect of melting snow in the river discharge (data not shown). (C) 1999 Elsevier Science B.V. All rights reserved.