In this study, the physical and chemical parameters at 0.5 m and 10 m water depth (e.g. temperature, salinity, density, pH, concentration of dissolved oxygen DO, nitrite NO2-, nitrate NO3- turbidity, alkalinity and total dissolved solid TDS) have been monitored by monthly field and laboratory measurements for 6 months in Kas Bay, Eastern Mediterranean. The measurements for nitrite, nitrate and dissolved oxygen concentrations were compared with the output of the zero dimensional water quality model. The model is a sub model of HYDROTAM-3D, which is an implicit baroclinic three dimensional model developed to simulate the wind driven circulations, hydrodynamics and basic water quality parameters in coastal waters. The numerical model has hydrodynamic, transport, turbulence as well as water quality components. The water quality component is based on a marine ecological submodel, aiming to simulate marine ecosystems. By using the general conservation equations, the nitrogen, phosphorus and the oxygen cycles were simulated in the ecological submodel as well as the dominant aquatic life forms, namely phytoplankton, zooplankton and the pelagic bacteria. In this paper, the model structure and the methods used by HYDROTAM-3D to simulate water quality parameters are presented together with a comparison of the model results and field observations in Kas Bay. (C) 2015 Elsevier Inc. All rights reserved.