The Lake Pertobe wetland system is a semi-natural wetland that has been modified primarily for recreational use. However, this lake system receives stormwater from much of the central business district of Warrnambool City (Victoria, Australia) and serves as a buffer zone between the stormwater system and the Merri River and Merri Marine Sanctuary. This work considers the impact of stormwater inputs on Lake Pertobe and the effectiveness of the lake in protecting the associated marine sanctuary. Sediment contaminants (including heavy metals and polycyclic aromatic hydrocarbons (PAHs)) and water quality parameters within the lake, groundwater and stormwater system were measured. Water quality parameters were highly variable between stormwater drains and rain events. Suspended solids rapidly settled along open drains and shortly after entering the lake. Groundwater inputs increased both salinity and dissolved nitrogen in some stormwater drains. Some evidence of bioaccumulation of metals in the food chain was identified and sediment concentrations of several PAHs were very high. The lake acted as a sink for PAHs and some metals and reductions in Escherichia coli, biological oxygen demand and total phosphorus were observed, affording some protection to the associated marine sanctuary. Nutrient retention was inadequate overall and it was identified that managing the lake primarily as a recreational facility impacted on the effectiveness of stormwater treatment in the system.