The coastline of eastern Georgian Bay in the Parry Sound region is a distinctive nearshore environment consisting of a large deep-water embayment partially isolated from the open lake and connected with other embayments of diverse morphometric features. The underlying geology of the embayments and their watersheds contrasts with the larger lake basin, resulting in heterogenous water quality stemming from mixing of the high-alkalinity, low phosphorus waters of Georgian Bay with the low-alkalinity and higher phosphorus waters draining watersheds of the Canadian Shield. In 2016, water quality was examined in the deep basin of Parry Sound known as the Big Sound, and six connected embayments to examine the influences of watershed loading and anthropogenic development to enable better detection of changes related to human activity. Inter-basin mixing and river loading accounted for much of the variability in major ions, water clarity and nutrients except for Deep Bay, an embayment exhibiting signs of nutrient enrichment. The oligotrophic conditions in Parry Sound have changed little since 1990 unlike Lake Huron where the dreissenid invasion has correlated with falling phosphorus levels. Low calcium levels may limit dreissenid mussel numbers in Parry Sound and are hypothesized to have pre-empted mussel-related changes in water quality. Apparent productivity, light regime and water column stratification of the Big Sound and connected embayments contrast with the adjacent nearshore of Georgian Bay indicating an aquatic environment distinct from the exposed nearshore of Georgian Bay.