SF Bay tributary spawning of Longfin Smelt

The longfin smelt (Spirinchus thaleichthys) was once one of the most abundant fishes in San Francisco Bay and Humboldt Bay and even supported a commercial bait fishery until the early 1970’s (Moyle 2002).

Like several pelagic fishes of the upper San Francisco Estuary, the longfin smelt experienced a marked decline since 2001, which contributed to its listing as “threatened” under the State Endangered Species Act [1](Baxter 2009; Sommer et al. 2007; CESA; Fish and Game Code §2050).  Many factors have been associated with this “pelagic organism decline” (POD) including increased freshwater diversions, decreased low-salinity habitat, reduced prey abundance, and frequent toxic algal blooms.  All of these impacts occur within larval habitats of the longfin smelt to various degrees (Armor et al. 2005; Feyrer et al. 2007b; Lehman et al. 2008; Sommer et al. 2007; Kimmerer et al. 2009). Despite the long-term decline in abundance of longfin smelt, the species has continued to exhibit a relatively strong abundance trend with freshwater outflow, as indexed by the spring mean position of X2.  The mechanism driving this relationship remains a key uncertainty in understanding the response of estuarine biota, including the longfin smelt, to management of freshwater flows.

Longfin Smelt have been found to utilize a variety of habitats including, freshwater, low-salinity, brackish and near shore ocean habitats throughout their 2-3 year life-cycle.  Larvae occur in freshwater to brackish habitats, whereas juveniles and sub-adults can be found throughout the SFE (Merz et al 2014; Hobbs et al. 2010).  Juvenile and adult Longfin Smelt are sensitive to warm water conditions (>18°C) in the summer-early fall,  and can be found evading warm waters by either residing in deep, cool, bay channel habitats or, exiting the SFE and residing in coastal marine habitats (Rosenfield and Baxter 2007).

Our current knowledge regarding spawning habitat is based on observations of catch by IEP surveys long-term monitoring surveys in Suisun Bay and the confluence of the Sacramento and San Joaquin River, and UC Davis surveys in Suisun Marsh.  Mature individuals have been observed in the Delta near the confluence of the Sacramento and San Joaquin rivers starting in December extending through March (Rosenfield and Baxter 2007).  Spawning is thought to occur in freshwaters upstream of the confluence of the Sacramento and San Joaquin rivers; however, recent evidence suggests that some Longfin Smelt may utilize low-salinity habitats in Suisun Bay and other Bay tributaries to spawn, particularly during wet years (Grimaldo et al. 2014).

As recently described by Cowin and Bonham (2013), a more complete understanding of the geographic extent of the population at each life stage and how various factors may influence monitoring results is needed to inform more effective management and protection of the species, including habitat restoration and water project operations. In a broad context, understanding the spatial distribution of spawning and successful recruit may elucidate the underlying mechanism driving the longfin smelt abundance-X2 relationship, as higher freshwater flows could enhance spawning and survival of longfin smelt utilizing tributaries to San Pablo Bay and South Bay.

In this study, the geographic distribution of maturing adults and larvae is being investigated by extending monitoring surveys into bay tributaries to San Pablo Bay including the Napa River and adjacent marsh, Sonoma Creek, the Petaluma River, and adjacent marsh and Coyote Creek and Alviso Marsh in Lower South Bay.