The Russian River Estuary in Sonoma County, California is a threatened ecosystem that provides an important habitat for salmonids (e.g. Coho salmon, Chinook salmon, and Steelhead trout) during several life stages. Periodically, the tidal inlet of the estuary is blocked when wave action overcomes tidal and river flows, creating a sand barrier. The resulting cessation of tidal mixing in the estuary causes persistent water column stratification between saline bottom‐waters and fresh surface waters. The bottom‐waters are then isolated from atmospheric oxygen inputs and dissolved oxygen declines, reducing available habitat for salmonids. To examine this problem, we compared time‐series data of dissolved oxygen levels during past closure events with directly‐measured biochemical oxygen demand (BOD) levels. We found that bottom‐water dissolved oxygen concentrations typically reached hypoxia (<3 mg/L) in lessthan four days. BOD levels in the estuary were highest in bottom‐waters, especially in deep scour‐holes upstream where water is trapped and riverine organic matter accumulates. Water column BOD due to the decomposition of organic matter accounted for a majority of observed oxygen consumption rates. We found little evidence of re‐oxygenation of the bottom‐water while the inlet remained closed (typically periods of less than 10 days). Although further study is required to determine oxygen dynamics throughout a longer closure period, the persistence of bottomwater hypoxia during the events we examined is an important consideration for estuary and watershed management.