Coastal eutrophication and bottom water hypoxia are stressors in many coastal and marine ecosystems, including the fjords and embayments of the Salish Sea. Recent work by researchers at Western Washington University and Northwest Indian College has identified a relatively large area (>10km2) of low dissolved oxygen (DO) in bottom waters of Bellingham Bay (Bellingham, WA) that returns predictably each summer. Direct measurements of water column respiration indicate that incoming oceanic deep water exhibits moderate rates of oxygen consumption (~100ug O2/L/d), yet manipulative experiments reveal that rates of respiration are carbon (rather than temperature) limited and respond quickly to additions of organic matter. This observation was corroborated by changes in bottom water respiration and DO in response to export of Pseudo nitzschia from surface blooms. Our research reveals the coupling between algal productivity and bottom water hypoxia, but also that this response is rapid and short lived. Further, we found that low DO water masses in Bellingham Bay are highly dynamic and appear to respond to upwelling events and high volumes of tidal flushing characteristic of many west coast estuaries.