Most of the water flowing through Lake Austin is from water released from the bottom of Lake Travis. As such, Lake Travis acts as a large settling pond, capturing many of the pollutants and sediments. As a result, the water coming into Lake Austin is very clear, allowing sunlight to penetrate 10-15 feet. This in turn is a contributing factor in Lake Austin's major water quality concern, which is excessive growth of aquatic weeds, particularly Eurasian Watermilfoil and Pondweed. While the aquatic plants are beneficial to fish, they quickly become a nuisance to lake users and lakeside property owners.
Town Lake is a relatively small water body that receives runoff from a large drainage area.
The contributing watershed consists of nine tributary creeks and numerous smaller drainage areas along the six-mile length of the lake. The total drainage area between Longhorn Dam and Tom Miller Dam is 158 square miles. The lake surface covers only 0.7 square miles or 477 acres. This results in continued impacts due to nonpoint-source pollutants. Sedimentation, pesticides and algae blooms continue to be a concern for Town Lake.