The longfin smelt, so-named for its long pectoral fins, lives in the open water of San Francisco Estuary. Source: U.S. Bureau of Reclamation

By James Hobbs and Peter Moyle
Another native fish of the Sacramento-San Joaquin Delta appears to be rivaling the cliffhanger status of the delta smelt.

Relative to its historical abundance, the lesser-known longfin smelt has experienced an even bigger decline than delta smelt — and may be in bigger trouble — according to trawl surveys of Delta fishes.

In the past two years, catches of adult longfins have been close to zero, and a recent larval survey found alarmingly few of the smelt. The dramatic downturn is likely a result of the drought, as with the tinier delta smelt.

Lacks federal protection

Unlike its headline-grabbing relative, the longfin is not listed under the federal Endangered Species Act.

In 2012 the U.S. Fish and Wildlife Service determined that the Delta population of longfin smelt deserved protection, but designated the fish only as a candidate for listing. The less powerful California Endangered Species Act lists the species as threatened with extinction. Presumably, the federal protections for the delta smelt have benefited the longfin and other native fishes because it is the species most sensitive to changes in the Delta’s waterways.

The longfin and delta smelt were once common, thriving inhabitants of the Delta and elsewhere in the open waters of San Francisco Estuary. The longfin live two to three years longer than the delta smelt and grow twice as big – up to 5 inches long – big enough to have been an important part of the San Francisco Bay commercial smelt fishery in the 19th century.

Longfin smelt grow up to 5 inches, about twice the length of nature delta smelt. Photo by Randall Baxter/California Department of Fish and Wildlife

The longfin population was the most abundant fish in the upper estuary. The population has gone through several boom and bust periods (Figure 1).

The initial slump, in the 1980s, was at least partially the result of the invasion of the overbite clam, which has robbed pelagic fish of food. Starting in 2002, the population nosedived, following the trajectory of delta smelt and other species — a trend known as the Pelagic Organism Decline. 

Sampling programs all show population collapsing

Before 1980, the state’s Fall Midwater Trawl survey alone would catch thousands of individuals in a four-month season (September-December). Since 2002, only 10 – 100 fish have been captured per season.

A similar pattern is shown in the San Francisco Bay Study, a monthly fish survey that uses midwater and bottom otter trawls to sample from South San Francisco Bay to the North Delta. Together, the state surveys show a dramatic decline of longfin smelt throughout the estuary (Figure 2).

Likewise, our monthly sampling in Suisun Marsh, which UC Davis began in 1979, has shown a long-term decline of the smelt (Figure 3).

Tom Cannon, an estuarine fisheries ecologist and biostatistician, was perhaps the first to sound the alarm over the estuary population of longfin smelt, in a recent California Fisheries Blog headlined, “They’re Gone.” 

Are they on the verge of extinction? The answer is not as clear as it seems to be for delta smelt, in part because so much less is known about longfin.

Recent UC Davis surveys have found longfin smelt in areas not previously monitored — Alviso Marsh in the lower South Bay, Napa-Sonoma Marsh, Petaluma River and the Cache-Lindsey Complex of the North Delta — raising the question of whether the smelt’s distribution has changed.

While the species clearly is in severe decline, it is possible that sampling programs are missing significant segments of the population. In summer and fall, substantial numbers inhabit coastal waters — outside areas surveyed.

However, all sampling programs within the estuary show longfin of all ages collapsing in the past few years,  suggesting an estuary-wide decline.

Drought impacts

The aggressive invasion of the overbite clam in San Francisco Estuary is blamed as one of the causes of the decline of delta and longfin smelt in recent years. Photo by Cynthia Brown/U.S. Geological Survey

The abundance of longfin smelt, particularly young-of-year, increases with the amount of freshwater flowing through the estuary (Figure 4). The fish also seems to have a low tolerance for warmer waters, with adults rarely found in water warmer than 64 degrees (18 degrees C) and young-of-year above 73 degrees (22 degress C) [Figure 5].

Warmer temperatures and less freshwater flow in the Delta are associated with drought, so if the drought continues, longfin smelt are likely to be extirpated from the estuary. Even if the drought ends, smelt numbers may be so low that recovery will be difficult and slow.

Recolonization from more northern populations is possible but highly uncertain, reflecting a need for more research on the basic biology of the species. We just hope the smelt will still be around to study.

James Hobbs is a research scientist and Peter Moyle if a professor of fish biology, both with the UC Davis Department of Wildlife, Fish and Conservation Biology. This article was originally posted on Aug. 31, 2015 and revised Sept. 1 with additional information and sources.

Further reading

Hobbs, J. A., C. Parker, J. Cook and M. Bisson. 2015. Technical Report: The distribution and abundance of larval and adult longfin smelt in the San Francisco Bay tributaries Year 1: Pilot Study. DOI: 10.13140/RG.2.1.3185.5843

Hobbs, J.A., L. L. Lewis, N. Ikemiyagi, T. Sommer and R. Baxter. 2010. “The use of otolith strontium isotopes (87Sr/86Sr) to identify nursery habitat for a threatened estuarine fish.” Environmental Biology of Fishes. 89:557-569. DOI 10.1007/s10641-010-9762-3

Merz, J.E., P.S. Bergman, J. F. Melgo and S. Hamilton. 2013. Longfin smelt: spatial dynamics and ontogeny in the San Francisco Estuary, California. California Fish and Game 99(3):122-148

Rosenfield, J. A. and R. Baxter. 2007. Population dynamics and distribution patterns of longfin smelt in the San Francisco Estuary. Transactions of the American Fisheries Society 136:1577-1592

Figure 1.  Fall Midwater Trawl Survey abundance indices for most common Delta fishes, 1967 – 2014. (Axes scaled to abundance of longfin smelt, with breaks in y-axis for less abundant species) Source: California Department of Fish and Wildlife

Figure 2.  Abundance indices (standardized) for longfin smelt, 1980 – 2014. Source: California Department of Fish and Wildlife 

Figure 3. Catch-per-minute otter trawling Suisun Marsh, 1980 – 2014. Source: UC Davis

Figure 4.  Longfin smelt abundance in Fall Midwater Trawl plotted against Delta freshwater outflow (log transformed). Regression lines for 1967 – 1987 (pre-overbite clam invasion); 1988 – 2000 (during invasion); and 2002 – 2014 (post-invasion). The invasive overbite clam has robbed food from longfin smelt and other pelagic species. Source: California Department of Fish and Wildlife

Figure 5.  Smoothed presence-absence data of longfin smelt — Age 0, Age 1 and Age 2 –with water temperature, 1980 – 2013. Source: San Francisco Bay Study (otter and midwater trawls)