Invasive species can produce complex and unpredictable effects across multiple trophic levels through a combination of direct and indirect pathways. Invasive silver carp (Hypophthalmichthys molitrix) exert substantial pressure on the link between primary production and intermediate trophic levels in large rivers of the Midwestern USA. The goal of our manuscript was to describe the silver carp population invasion in the Illinois River (Illinois, USA) and explore the potential effects of silver carp on the native biota. We obtained 22 years of data from three long‐term monitoring programmes for phytoplankton, zooplankton, and age‐0 and adult native fishes. To determine when silver carp started affecting native biota, we used nonlinear regression to estimate the change point in silver carp biomass. We then used piecewise linear regression to separately model the response of phytoplankton and age‐0 and adult native fishes, using the model‐estimated change point in silver carp biomass. We tested for differences in taxon‐specific zooplankton density and biomass between pre‐ and post‐establishment periods using generalised linear models. To explore associations between native biota, silver carp and other potential drivers, we used single‐factor linear‐regression models in an information theoretic‐based approach. Our analysis showed individual silver carp condition decreased while their population numbers and biomass increased during their establishment in the Illinois River. Concurrently, analysis of 22 years of producer and consumer abundance and biomass data shows phytoplankton density and macrozooplankton density and biomass decreased—zooplankton by over 90%—during the same period, though the responses of age‐0 native fish biomass and adult native fish biomass were more nuanced. Our study provides compelling evidence of multiple trophic‐level effects from the silver carp invasion in North America and highlights the importance of long‐term data collection and monitoring. Our research shows managers that zooplankton and perhaps phytoplankton are quickly and negatively affected by silver carp, which may eventually cascade into higher trophic levels over longer timescales.

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Large riverine landscapes are among the most productive ecosystems on earth, and the most affected by humans. Few studies explicitly explore the effects of, or responses to, multiple stressors in highly modified large river systems. Changes in fish assemblages in response to multiple anthropogenic stressors were explored from a 60-year data set for the Illinois River (Illinois, USA). Despite a legacy of stressors, the highly modified Illinois River responded to additional multiple stressors, especially four distinct stressor phases, which included two policies to improve water quality and bigheaded carp invasion. The response in fish diversity (Shannon H′) was complex in terms of the number of thresholds in the pattern of fish diversity, the rate and direction of change between thresholds, and the variance of response at two spatial scales and two ecological levels of organization. Overall, nine response trajectories were observed. Changes in fish diversity in the Illinois River since 1959 do not conform to current ecosystem response models. Without long-term and broad-scale data, elucidating complex responses in large river ecosystems is unlikely. Expanding the spatial and temporal scale of investigation in modified large rivers will increase our ability to understand how these ecosystems respond to multiple stressors.