Water quality was assessed for five subregions of Lake Oconee and Lake Sinclair in Georgia, USA. The areas were chosen for their levels of human impact, including: (i) suburban development >30 years old; (ii) modern suburban development; (iii) industry; (iv) agriculture; and (v) an area of low human activity. The measured temperature, pH, dissolved oxygen concentration and turbidity values were normal for oligotrophic lakes. Faecal pollution in the lakes was determined using the membrane filtration method (Method 1600) on mEI plates for enterococci. There was a positive correlation between turbidity and the number of faecal enterococci in the lakes. The faecal pollution level was higher for the old suburban and agricultural areas. Faecal pollution in the agricultural region of Lake Oconee exceeded EPA regulatory standards. The faecal pollution source was identified using polymerase chain reaction detection, with Bifidobacterium adolescentis being a marker of human faecal pollution, and bovine-associated Bacteroides (BoBac) as a marker of cattle faecal pollution. Human faecal pollution was detected in the agricultural, old suburban and industrial areas of the lakes. In contrast, bovine faecal pollution was detected only in the agricultural area of Lake Oconee. Measurements of chlorophyll-a and relative algal community abundance indicated the least-impacted and modern suburban areas had significantly lower numbers of primary producers, being dominated by diatoms.