Rivermouth regions such as the Milwaukee Harbor, are the habitat interface between watersheds and the Great Lakes proper, and can host a large diversity of fishes. To facilitate an ecosystem approach management strategy, I developed a layered map that includes bathymetry, side scan sonar images, shoreline substrate classifications, and initial data of aquatic vegetation and centrarchid spawning locations. The 60 km perimeter of the study area consisted of 59% hardened shoreline. Ground truthing of substrate classifications via Ponar grabs or video had about 95% accuracy for fine and rocky boulder substrates. Rocky fine was the most inaccurate classification (35%), but with the introduction of a new classification "mussels fine," it improved to 90.8%. The Milwaukee Estuary shoreline area was dominated by fine substrate particles (69.52%), with the next most common categories being rocky boulder (10.65%) and wood/steel pilings (9.51%). Six species of centrarchids were found to reproduce at various times in five locations. Macrophytes were sampled in 28 separate locations in four pre-determined areas. Eight different species of aquatic plants were collected and identified. Likely challenges for creating a more ecologically functional harbor for fishes will be to develop nursery habitats in a significantly altered environment and enhance habitat connectivity.