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Abstract Networks of direct and indirect biotic interactions underpin the complex dynamics and stability of ecological systems, yet experimental and theoretical studies often yield conflicting evidence regarding the direction (positive or negative) or magnitude of these interactions. We revisited pioneering data sets collected at the deciduous forested Horonai Stream and conducted ecosystem‐level syntheses to demonstrate that the direction of direct and indirect interactions can change depending on the timescale of observation. Prior experimental studies showed that terrestrial prey that enter the stream from the adjacent forest caused positive indirect effects on aquatic invertebrates during summer by diverting fish consumption. Seasonal and annual estimates of secondary production and organic matter flows along food web pathways demonstrate that this seasonal input of terrestrial invertebrate prey increases production of certain fish species, reversing the indirect effect on aquatic invertebrates from positive at the seasonal timescale to negative at the annual timescale. Even though terrestrial invertebrate prey contributed 54% of the annual organic matter flux to fishes, primarily during summer, fish still consumed 98% of the aquatic invertebrate annual production, leading to top‐down control that is not revealed in short‐term experiments and demonstrating that aquatic prey may be a limiting resource for fishes. Changes in the direction or magnitude of interactions may be a key factor creating nonlinear or stabilizing feedbacks in complex systems, and these dynamics can be revealed by merging experimental and comparative approaches at different scales. 

Abstract Habitat enhancements seek to ameliorate the detrimental effects of environmental degradation and take many forms, but usually entail structural (e.g. logs, cribs, reefs) or biogenic (e.g. carrion additions, vegetation plantings, fish stocking) augmentations with the intent of increasing fish annual production (i.e. accrual of new fish biomass through time). Whether efforts increase fish production or simply attract fish has long been subject to debate.Streams of the Pacific Northwest are commonly targeted for habitat enhancements to mitigate for the detrimental effects of dams and other forms of habitat degradation on Pacific salmon. Nutrient mitigation (i.e. the practice of artificially fertilising freshwaters) is a form of biogenic habitat enhancement that attempts to mimic the enrichment effects of a natural Pacific salmon spawning event. This approach assumes nutrient augmentations alleviate nutrient limitation of primary producers and/or food limitation of primary and secondary consumers, culminating in increased fish production.We conducted a multi‐year manipulative experiment and tracked responses of interior rainbow trout (Oncorhynchus mykiss) to annual additions of Pacific salmon carcasses as part of an effort to enhance the productivity of salmonid populations in streams where salmon runs have been lost. We employed an integrated approach to partition the mechanisms driving numerical responses of trout populations across timescales, to assess population turnover, and to track responses to habitat enhancements across individual to population level metrics.Short‐term numerical increases by trout were shaped by immigration and subsequently via retention of individuals within treatment reaches. As trout moved into treated stream reaches, individuals foraged, grew, and subsequently moved to other locations such that short‐term increases in fish numbers did not persist from year to year. All told, additions of salmon carcasses alleviated apparent food limitation and thereby increased secondary production of rainbow trout. However, at an annual time scale, increased production manifested as larger individual fish, not more fish within treated reaches. Fish movements and high population turnover within treated stream reaches apparently led to the subsequent dispersal of increased fish production.We found multiple lines of evidence that indicated that annual additions of salmon carcasses aggregated rainbow trout and enhanced their annual production. Through this replicated management experiment, we documented dynamic individual and population level responses to a form of stream habitat manipulation across weekly and annual timescales.