Population dynamics and distributional patterns of longfin smelt in the San Francisco Estuary. Transactions of the American Fisheries Society 136:1577–1592

Abstract.—The San Francisco Estuary supports several endemic species of fish and the southernmost populations of other species. Many of these native species and populations are imperiled or have experienced recent population declines that indicate a general decline in the estuary’s capacity to support pelagic fish species. We studied the distribution and abundance of one of the estuary’s native species, longfin smelt Spirinchus thaleichthys, using data from three long-term aquatic sampling programs. Each of the sampling programs we studied revealed a substantial reduction in the abundance of longfin smelt. These trends support the idea that the estuary’s capacity to support pelagic fish species has been significantly reduced over the past three decades. Longfin smelt in the estuary displayed consistent patterns in relative abundance and distribution during their life cycle. We also found significant, but weak, spatial autocorrelation among sampling stations. These patterns in distribution reveal differential habitat use and migratory behavior. Managers can use these insights into longfin smelt distribution patterns to improve interpretation of sampling program results. The San Francisco Estuary is one of the largest estuaries in North America, covering approximately 1,235 km2. The estuary drains about 40 % of Cal