Environmental history recorded in sediments can track estuarine water quality through the use of geochemical and biological proxies. I collected sediment cores from two locations in the Coos Bay Estuary, at South Slough and Haynes Inlet, spanning from ~1680 AD to the present. To address the historical water column oxygen in the estuary I measured geochemical proxies including organic matter, magnetic susceptibility, and redox-sensitive metals to calibrate against a detailed 15-year record of dissolved oxygen observations. High visual correlation of these proxies and recent water quality supports the interpretation of long-term water quality from sediment cores. Finally, I provide evidence that potential low water quality has increased at South Slough, while decreasing or staying stable at Haynes inlet over the last 300 years. This history was explained by changing land use (logging, splash dams) effects on erosion and organic matter and the role of the dredged channel.