A brief overview of Lower San Joaquin River flow objectives

For about a decade, experimental studies have been conducted on the lower San Joaquin River as part of the Vernalis Adaptive Management Plan (VAMP).  The goal is to gather data about how changes to inflow and exports affect the survival of Chinook salmon smolts that migrate from the San Joaquin, through the Delta, and out to the Pacific Ocean.  Along that migration path, salmon encounter a complicated obstacle course blocking their path to the sea, including predators and confusing reverse flows caused by export pumping.  Improving our understanding about how salmon respond to this altered environment is necessary if once-abundant fisheries are to be restored.

Delta flow objectives and export limits have evolved over the years.  A water quality control plan was issued in 1995 after the Bay Delta Accord, and it attempted to achieve, among other things, salmon doubling.  The plan provided various objectives relating to operation of the Delta Cross Channel gates, outflow, exports, dissolved oxygen, and salinity.  It also stated varying flow objectives for rivers, including the San Joaquin River at Vernalis.  Pulse flows were to be provided to facilitate migration of salmon in the San Joaquin system.  Depending on water year type, average flows from approximately April 15 to May 15 were set to somewhere between 3,110 and 8,620 cfs.  Export limits during that same time period were generous: the larger of 1,500 cfs or a three-day running average of conditions at Vernalis.

In 2000, the State Board incorporated into Decision 1641 the San Joaquin River Agreement, which did not propose to provide flows entirely consistent with those originally prescribed.  The agreement established a framework to implement the Vernalis Adaptive Management Plan (VAMP), a twelve-year experimental program starting in 2000 that would study the effects of flows, exports, and the Head of Old River Barrier on survival of salmon smolts as they move down the San Joaquin River and through the Delta.  VAMP was characterized as an “initial stage” in the process of achieving spring pulse flow objectives.  Exchange contractors and tributary irrigation districts would provide releases to implement these targets.  In conjunction with export reductions, the study would achieve no worse than a 2:1 flow-export ratio (a parameter from the biological opinions):

The biological opinions were later revised to comply with court rulings.  The 2009 revision of the NMFS biological opinion includes an action measure (Action IV.2.1) that is to be implemented for the two-month period from April 1 to May 31, fully containing the VAMP period.  This doubles the time in which migrating salmon and steelhead are afforded additional protection.  Action IV.2.1 has two main requirements.  First, it sets minimum Vernalis flows based on storage at New Melones Reservoir.  Second, it requires that combined federal and state exports be limited to a fraction of Vernalis flows:

In a May 2010 ruling, Judge Wanger specifically took issue with the inflow-export ratio.  He also took issue with Action IV.2.3, which limits negative/reverse Old and Middle River flows, from January 1 to June 15, to somewhere between -2,500 and -5,000 cfs.  Contractors have protested both the salmonid and delta smelt biological opinions because they limit export pumping.  Wanger granted them relief, for basically these reasons:

1.  NMFS and Reclamation violated NEPA because the agencies failed to prepare an EIS documenting the environmental impacts of protecting the environment (i.e. fish);
2.  The harm to Westlands and the “human environment” — theoretically caused by decreased exports — was more compelling during this short-term period than the effects on fish of increasing exports; and
3.  He was dissatisfied with the quality of scientific analysis applied by the resource agencies.

More on the VAMP studies, and some belated thoughts on the latest Wanger decisions, to come in future posts.