This paper presents the initial environmental effects of polyaluminum chloride application on the water quality of two connected, shallow urban lakes in the Mazurian Lakeland, Poland. The water quality of Lake Domowe Duże (62 ha, mean depth 2.4 m) and Lake Domowe Małe (11 ha, mean depth 2.8 m) in Szczytno did not improve after sewage discharge cutoff. Thus, local authorities decided to implement a restoration project involving the 3-year application of aluminum coagulant (26 g Al m−2) and manipulation of fish stocking. In 2010 and 2011, the first two stages of the project were conducted. After restoration measures, phosphorus concentration in water, chemical oxygen demand, chlorophyll ‘a’ and phytoplankton biomass decreased significantly compared to the control years. No long-term decrease of pH was obtained after aluminum application. Low concentrations of dissolved aluminum in a water column (below 0.2 mg L−1 during technical operations) did not show any negative effects on aquatic fauna.