The long-term variation in flow velocity, temperature and salinity fields in the Ise-Mikawa Bay estuary was examined in a triennial simulation, using a time-dependent 3-D hydrodynamic model. The simulation covered from April 1993 to March 1996. The daily change regimes of the observed sea-surface winds, tidal elevation at the open boundary, river discharges and meteorological parameters were incorporated into the forcing variables of the modelled estuary. Simulated distributions of temperature and salinity were compared favorably with the field measurements both in time and space, suggesting good reproducibility of the flow field by the hydrodynamic model. The numerical results were compared favorably with the field measurements of water quality indicating the validity and predictive capability of the model, and thus served for a detailed analysis of nutrient and oxygen cycles in the estuary. It turned out from the nutrient flux analysis that primary productivity varied considerably over the three years in relation to water temperature and that the most limiting nutrient to phytoplankton growth was nitrogen. The oxygen field in the bottom layer, on the contrary, did not show any clear year-to-year variation in that the oxygen-depleted water mass regularly appeared in the middle-upper basin from late June, developed to cover the whole middle-upper basin in midsummer, and dissipated by about mid-November.