Abstract
The Stockton Deep Water Ship Channel, a stretch of the tidal San Joaquin River, is frequently subject to low dissolved oxygen conditions and annually violates regional water quality objectives. Underlying mechanisms are examined here using the long-term water quality data, and the efficacy of possible solutions using time-series regression models. Hypoxia is most common during June-September, immediately downstream of where the river enters the Ship Channel. At the annual scale, ammonium loading from the Regional Wastewater Control Facility has the largest identifiable effect on year-to-year variability. The longer-term upward trend in ammonium loads, which have been increasing over 10% per year, also corresponds to a longer-term downward trend in dissolved oxygen during summer. At the monthly scale, river flow, loading of wastewater ammonium and river phytoplankton, Ship Channel temperature, and Ship Channel phytoplankton are all significant in determining hypoxia. Over the recent historical range (1983–2003), wastewater ammonium and river phytoplankton have played a similar role in the monthly variability of the dissolved oxygen deficit, but river discharge has the strongest effect. Model scenarios imply that control of either river phytoplankton or wastewater ammonium load alone would be insufficient to eliminate hypoxia. Both must be strongly reduced, or reduction of one must be combined with increases in net discharge to the Ship Channel. Model scenarios imply that preventing discharge down Old River with a barrier markedly reduces hypoxia in the Ship Channel. With the Old River barrier in place, unimpaired or full natural flow at Vernalis would have led to about the same frequency of hypoxia that has occurred with actual flows since the early 1980s.
Highlights
The lower San Joaquin River, one of two major rivers draining into the San Francisco Estuary, is frequently subject to low dissolved oxygen conditions and annually violates regional water quality objectives
Hypoxia in the San Joaquin River is most frequent from Lights 40 through 43 in August and September; it occurred at this time and region 60% to 80% of the time in the existing historical record
The data are useful for examining the relationship between surface (i.e., 1 m depth) and bottom dissolved oxygen. This relationship is important for understanding the relevance of the continuous dissolved oxygen monitoring data, which represent water collected from a single depth at 1 m. (The intake is enclosed and protected by a vertical perforated pipe extending from 1 to 5 m, approximately, so the sample integrates 4 m of the water column.) We focus on stations L40, L41, and L43, which encompass the location of the continuous sensor and are the locations of most intense hypoxia
Summary
The lower San Joaquin River, one of two major rivers draining into the San Francisco Estuary, is frequently subject to low dissolved oxygen conditions and annually violates regional water quality objectives. The violations usually occur between June and November over a 20-km river reach immediately downstream of the city of Stockton. This reach is part of the Stockton Deep Water Ship Channel, a portion of the river between San Francisco Bay and the city that has been dredged to allow the passage of ocean-going vessels to the city’s port. Dissolved oxygen concentrations can be chronically below regional water quality objectives and reach below 2.5 mg L-1 at times These low oxygen conditions interfere with several beneficial uses of the river, including spawning and migration of both warm (striped bass, sturgeon, and shad) and cold (salmon and steelhead) freshwater fishes, as well as warm and cold freshwater species habitat (CVRWQCB 2003). Low dissolved oxygen has recently been severe enough to kill both steelhead and salmon, as reported in The Record (Stockton), 8 July 2003
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