Lake Uluabat is one of the most important wetlands in Turkey because of its rich biodiversity, lying on a migratory bird route with almost all its shores being covered by submerged plants. The lake has been protected by the Ramsar Convention since 1998. However, the Lake is threatened by natural and anthropogenic stressors as a consequence of its location. Geographic Information System (GIS) analysis is a tool that has been widely used, especially for water quality management in recent years. This study aimed to investigate the water quality and determined most polluted points using GIS analysis of the lake. Temperature, pH, dissolved oxygen, chemical oxygen demand, Kjeldahl nitrogen, total phosphorus, chlorophyll-a, arsenic, boron, iron, and manganese were monitored monthly from June 2008 to May 2009, with the samples taken from 8 points in the lake. Effect of pH, relation of temperature, and Chl-a with other water quality parameters and metals are designated as statistically significant. Data were mapped using ArcGIS 9.1 software and were assessed according to the Turkish Water Pollution Control Regulations (TWPCR). The research also focused on classifying and mapping the water quality in the lake by using the spatial analysis functions of GIS. As a result, it was determined that Lake Uluabat belonged to the 4th class, i.e., highly polluted water, including any water of lower quality. A remarkable portion of the pollution in the water basin was attributed to domestic wastewater discharges, industrial and agricultural activities, and mining.