<p> This thesis reports the results of a study that aims to develop and implement a simple, yet effective substrate identification and classification scheme for the Owen Sound and Colpoy' s Bay region of southern Georgian Bay using side scan sonar data. Documentation of substrate types in the study area is required to enhance fish rehabilitation programs conducted by the Ontario Ministry of Natural Resources. Over 500km of side scan sonar data and 1 OOkm of sub-bottom seismic data were collected in Owen Sound and Colpoy' s Bay during the summer of 2004. Analysis of the side scan images allowed identification of seven substrate types in the two bays including mud (Facies 1), sand (Facies 2), sand with ripples or dunes (Facies 3 and 4), sand with boulders (Facies 5), boulder rich lake floors (Facies 6) and bedrock (Facies 7). Patches of aquatic vegetation could also be identified on the images. Sub-bottom seismic data collected concurrently with the side scan data were used to validate interpretations of substrate type made from side scan images. This substrate identification system appears to serve as a rapid and cost-effective method of determining substrate characteristics based solely on the geophysical properties of acquired sonar and seismic data. </p> <p> Lake floor sediment distribution maps of Owen Sound and Colpoy' s Bay were subsequently created from the side scan data using both a computer-based and a more traditional hand-drawn technique. The hand-drawn mapping technique integrated interpretation of side scan images with sub-bottom seismic data and pre-existing knowledge of bathymetry, shoreline sediment types and environmental factors and appears to present the most realistic delineation of surface sediment distributions in Owen Sound and Colpoy's Bay. Substrate types within both bays can be subdivided into three distinct zones; Zone 1 is mud-rich and lies in water depths greater than 30m; Zone 2 includes sand dominated substrates and is found in water depths of between Om and 40m and Zone 3, found on exposed shoals and in shallow water areas consists of the coarsegrained gravel and bedrock substrates preferred as fish spawning grounds. </p> <p> This is the first side scan study to have been conducted in southern Georgian Bay and the results can be used to more effectively plan and design fish rehabilitation and restoration projects in the region. </p> / Thesis / Master of Science (MSc)