Unique ecosystems described as “estuaries” form where rivers meet the sea. Upstream changes in land use and land cover impact the quality and quantity of riverine flows to estuarine environments, in turn leading to degradation of many nearshore habitats. Oyster reefs are one example of an estuarine system experiencing widespread degradation due to changes in riverine waters. Oysters provide important ecological benefits to estuarine systems, and their degradation is believed to drive large-scale changes in estuarine water quality. We are using satellite imagery to characterize these large-scale relationships between upstream change, river flow, and oyster reef health. As a case study site, we are focusing on the Suwannee River Estuary, which is home to miles of threatened oyster reefs and showcased here in a USGS Landsat8 image. The blackwaters of the Suwannee breathtakingly contrast with the greenish-blue waters of the Gulf of Mexico.