The physical, microbiological quality parameters and plankton abundance have been monitored and evaluated in coastal waters of Fethiye Inner Bay, Turkey. The temporal and areal variations of quality parameters have been investigated through the monthly measurements at 14 locations between March 2016 and February 2017. The physical parameters measured throughout the water column were water temperature, salinity, pH, and turbidity. Besides, water samples were taken from the surface waters, and total coliform, fecal coliform, fecal streptococci, Escherichia coli, Pseudomonas aeruginosa, Salmonella detection, phytoplankton and zooplankton abundance analyses were performed in the laboratory. By using the related Turkish Standards Institution (TSE) standards, biochemical oxygen demand and dissolved oxygen levels were also determined. Results were evaluated to understand the microbiological water quality of Fethiye Inner Bay, by the Turkish Regulations for the Surface Water Quality (2016) and the Quality of Bathing Water (2006), and Directive 2006/7/EC on bathing water. For the evaluation of the results, geographic information systems (GIS) based HYDROTAM-3D that is the first coastal waters hydrodynamic, transport and water quality model developed in Turkey, was used (http://www.hydrotam3d.com/fethiye). A microbiological parameters database was established for Fethiye Inner bay coastal waters by using HYDROTAM-3D model water quality management system, accessible over the internet.