Upstream and inshore regions of the Maryland Coastal Bays exhibit degraded water quality. Six streams and three shallow bays were sampled in May and July 2006 and 2007 to compare spatial patterns in relation to land use and nutrient loading. St. Martin River, having a high percentage of crop agriculture and a low percentage of forest and wetlands, experienced the most degraded water quality of the three regions, and stream total nitrogen in its watershed was linked to feeding operations and anthropogenic land use. Despite having a much less developed watershed, Johnson Bay experienced degraded water quality, especially in inshore regions. Sinepuxent Bay had the best water quality of the three bays, but still demonstrated anthropogenic impacts. Nutrient loading from land use is directly related to the observed patterns in St. Martin River, while residence time, groundwater flows, and within-bay cycling has led to water quality degradation in Johnson Bay.