Attempts to develop open sea fish farming projects in the Black Sea have often failed due to poor site selection. This problem can be solved by using the Geographic Information System (GIS) to collect, manipulate, query, display, and integrate various data sets. In this study, data sets were arranged together to analyze habitats and a site selection methodology was developed for the coastal region of Trabzon on the Surmene Bay. Data included temperature, salinity, and current velocity, collected during regular cruises of the KTU-R/V Denar-I research vessel. Shoreline data were digitized using regional maps and spatial relationships were examined using Boolean Algebra. Two interpolation methods (Kriging and Inverse Distance Weight) were used to form thematic maps and identify optimal sites for a rainbow trout cage farm. No significant differences were found between the results of the two methods. Temperature was the most influential factor determining the final site position.