Land cover in the watershed is a mix of rural and urban uses. Overall, the watershed is about 33 percent urban, with agriculture (25%), grasslands (21%), forests (12%) and wetlands (6%) making up the rest of the major land cover types. Fourteen citites and villages are found in this watershed.

As with the other watersheds in the basin, the streams in the Milwaukee River South watershed exhibit a wide range of quality. Over 35 stream miles within the Milwaukee South Watershed are listed on the 303(d) list (Table 1, page 4), including the Milwaukee Estuary, a Great Lakes Area of Concern. The Milwaukee Estuary area of concern encompasses the Milwaukee Harbor, the Milwaukee River downstream from the abandoned North Avenue Dam, the Menomonee River downstream from 25th street and the Kinnickinnic River downstream from Chase Avenue. The international Joint Commission (IJC) and U.S. EPA designated the Milwaukee Estuary in 1987 through the Great Lakes Water Quality Agreement as one of 43 Great Lakes Areas of Concern. These areas are usually industrial in nature, with a history of pollution. In the Milwaukee Estuary, sediments contaminated with polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals are linked to degraded water quality, impaired fish and wildlife populations, and restrictions on dredging. A remedial action plan defining the problems with the estuary was published in 1989 by WDNR. A follow up plan further refining impairments and outlining a plan for restoring the estuary was published by WDNR in 1995.