Many regions around the Great Lakes have been designated Areas of Concern as a result of consistent water quality problems from pollutants like phosphorus and Escherichia coli, which cause eutrophication, beach postings and Beneficial Use Impairments. While foreshore beach sand is a potential reservoir for E. coli, there is less understanding of whether it might also be a reservoir and source of phosphorus for adjacent beach waters. We measured levels of E. coli, total phosphorus and soluble reactive phosphorus at Sunnyside and Rouge Beaches in the Toronto and Region Area of Concern, and stormwater outfalls in the adjacent Humber and Rouge Rivers within their beachsheds. Additionally, we used microbial source tracking assays to detect human and gull fecal contamination. Soluble reactive phosphorus concentrations were highest in stormwater outfalls, with concentrations as high as 556 µg l−1 at an outfall in the Sunnyside beachshed, and 4780 µg l−1 at an outfall in the Rouge beachshed. In contrast, the highest total phosphorus concentrations were typically found in foreshore beach sand pore water and were more associated with gull fecal contamination. Beach sand total phosphorus levels were as high as 10,600 µg l−1 at Sunnyside Beach, although the highest total phosphorus concentration measured (25,600 µg l−1) was in a Rouge River outfall. Concentrations of total phosphorus in outfalls were significantly correlated with concentrations of E. coli in both beachsheds and the human microbial source tracking marker in the Sunnyside beachshed outfalls. These results indicate that stormwater outfalls with sewage cross-contamination can deliver high concentrations of total phosphorus, soluble reactive phosphorus and fecal bacterial contamination to associated beachsheds. Further, similar to E. coli, foreshore beach sand can act as a reservoir of total phosphorus and a source for adjacent water bodies via wave action or groundwater discharge. High phosphorus inputs from beach sand could contribute localized changes to microbial communities and unique eutrophication effects along beach shorelines.