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While there is substantial information about the upstream migration of commercially and recreationally important fishes, relatively little is known about the upstream migration of small-bodied species, particularly through estuaries. In the San Francisco Estuary, there is a major need to understand the behavior of delta smelt Hypomesus transpacificus, a small pelagic fish listed under the state and federal endangered species acts. The spawning migration period may be critical as upstream movements can result in entrainment in water diversions. In general, delta smelt live in the low-salinity zone of the estuary and migrate upstream for spawning. During the fall pre-migration period, delta smelt remain primarily within the low-salinity zone in the western Sacramento-San Joaquin Delta and Suisun Bay. There were no significant upstream shifts of fish into fresher water during late fall, suggesting that delta smelt do not show pre-migration staging behavior. Following winter "first flush" flow events that appear to trigger migration, upstream movement rates are relatively rapid, averaging 3.6 km d -1 , a finding consistent with results from particle-tracking simulations, laboratory studies, and other fishes. Like some other native fishes, delta smelt apparently "hold" in upstream areas following migration; most do not spawn immediately. Overall, delta smelt fit the pattern of a diadromous species that is a seasonal reproductive migrant. Emerging data suggest that there is variability in the migration behavior of delta smelt, a pattern contrary to the reigning viewpoint that all smelt migrate in winter.

While there is substantial information about the upstream migration of commercially and recreationally important fishes, relatively little is known about the upstream migration of small-bodied species, particularly through estuaries. In the San Francisco Estuary, there is a major need to understand the behavior of delta smelt Hypomesus transpacificus, a small pelagic fish listed under the state and federal endangered species acts. The spawning migration period may be critical as upstream movements can result in entrainment in water diversions. In general, delta smelt live in the low-salinity zone of the estuary and migrate upstream for spawning. During the fall pre-migration period, delta smelt remain primarily within the low-salinity zone in the western Sacramento-San Joaquin Delta and Suisun Bay. There were no significant upstream shifts of fish into fresher water during late fall, suggesting that delta smelt do not show pre-migration staging behavior. Following winter "first flush" flow events that appear to trigger migration, upstream movement rates are relatively rapid, averaging 3.6 km d -1 , a finding consistent with results from particle-tracking simulations, laboratory studies, and other fishes. Like some other native fishes, delta smelt apparently "hold" in upstream areas following migration; most do not spawn immediately. Overall, delta smelt fit the pattern of a diadromous species that is a seasonal reproductive migrant. Emerging data suggest that there is variability in the migration behavior of delta smelt, a pattern contrary to the reigning viewpoint that all smelt migrate in winter.

Summary In stream ecosystems, Pacific salmon deliver subsidies of marine‐derived nutrients and disturb the stream bed during spawning. The net effect of this nutrient subsidy and physical disturbance on biological communities can be hard to predict and is likely to be mediated by environmental conditions. For periphyton, empirical studies have revealed that the magnitude and direction of the response to salmon varies from one location to the next. Salmon appear to increase periphyton biomass and/or production in some contexts (a positive response), but decrease them in others (a negative response). To reconcile these seemingly conflicting results, we constructed a system dynamics model that links periphyton biomass and production to salmon spawning. We used this model to explore how environmental conditions influence the periphyton response to salmon. Our simulations suggest that the periphyton response to salmon is strongly mediated by both background nutrient concentrations and the proportion of the stream bed suitable for spawning. Positive periphyton responses occurred when both background nutrient concentrations were low (nutrient limiting conditions) and when little of the stream bed was suitable for spawning (because the substratum is too coarse). In contrast, negative responses occurred when nutrient concentrations were higher or a larger proportion of the bed was suitable for spawning. Although periphyton biomass generally remained above or below background conditions for several months following spawning, periphyton production returned quickly to background values shortly afterwards. As a result, based upon our simulations, salmon did not greatly increase or decrease overall annual periphyton production. This suggests that any increase in production by fish or invertebrates in response to returning salmon is more likely to occur via direct consumption of salmon carcasses and/or eggs, rather than the indirect effects of greater periphyton production. Overall, our simulations suggest that environmental factors need to be taken into account when considering the effects of spawning salmon on aquatic ecosystems. Our model offers researchers a framework for testing periphyton response to salmon across a range of conditions, which can be used to generate hypotheses, plan field experiments and guide data collection.

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