The Sinissippi Lake watershed is a large watershed, about 237 square miles, which includes the mainstem of the Rock River from the dam at Horicon downstream to the Watertown dam and all the streams which flow into the Rock in this reach.
Land use is predominantly agricultural.
The watershed includes most of the city of Horicon, about half the City of Watertown, and the communities of Iron Ridge, Juneau, Hustisford, Clyman, Lebanon and Ixonia. Each of these communities has a municipal wastewater discharge in the watershed. Watertown is experiencing the most significant urban growth in the watershed. Overall, there are numerous wetlands adjacent to the watershed's streams, although significant wetland drainage has occurred. Two fish on the Wisconsin Threatened and Endangered Species lists have been found in the watershed.