One of the primary focuses of the MLA is to invest in the quality of the lake itself. They started with the contemporary Water Quality Initiative in 2000, however "early MLA water testing began in 1972"; over 100 volunteers, in 2013, collected water samples from designated sites in order to facilitate this initiative. These samples are used to analyze various bacteria counts in the water, the amount of dissolved organic carbon, phosphorus, temperature trends, and calcium. In 2013 the MLA collected over 1100 water samples from the Muskoka area. As seen in the 2013 Water Quality Report, the Muskoka Lakes Association focuses on 18 key areas affecting the Lake Muskoka region: Alport Bay, Arundle Lodge, Bala Bay, Beaumaris, Boyd Bay, Browning Island, Dudley Bay, East Bay, Eilean Gowan, Muskoka Bay, Muskoka Sands, North Bay, Stephen's Bay, Taylor Island, Walker's Point, Whiteside Bay, and Willow Beach.