Different forms of land uses (e.g. agriculture, tourism, recreational, industrial, housing) have detrimental impacts on water bodies (e.g. rivers, lakes, coastal waters). Thus, comprehensive land use plans developed integrating water quality models would certainly provide better solutions for the sustainability of natural water resources. In this study, the inner bay of Fethiye, located along the south-west coast of Turkey, is selected as a case to identify the land use and water quality relationship. At six locations in the Bay, various physical and chemical parameters (e.g. temperature, density, salinity, pH, concentrations of dissolved oxygen, nitrite, nitrate and total dissolved solid) were monitored by monthly field and laboratory measurements for four months during summer and autumn seasons. The measured nitrite, nitrate and dissolved oxygen concentrations were then compared with the estimations of the water quality sub model of HYDROTAM-3D, which is an implicit baroclinic 3D numerical model developed to simulate hydrodynamics, transport processes and basic water quality parameters in coastal waters. The paper presents results on monitored water quality parameters and model estimations, and discusses the sea water quality of the inner bay of Fethiye emphasizing the impacts of land use patterns in the town.