The Great Lakes, the largest surface freshwater resource in the world, has long been recognized for its valuable natural resources and services vital to the wellbeing of our nation. In 2012 a probabilistic sampling component was included under an expanded version of NOAA’s National Status and Trends/Mussel Watch Program in the Great Lakes as a basis for assessing the status of ecological condition and potential stressor impacts in targeted river and harbor systems of this important region. The probabilistic sampling is intended to provide managers and other stakeholders with information on the spatial extent of healthy versus unhealthy condition within these areas and the ability to quantify potential changes in their quality over time. Accordingly, in August 2012 a survey was conducted within a Great Lake’s sub-system, the Milwaukee Estuary in Wisconsin, which had been identified as an Area of Concern (AOC) relative to various Beneficial Use Impairment (BUI) designations. The present report presents results of that Milwaukee Estuary survey.