Abstract – Recent work demonstrates that tributary inputs are important community reorganisation points for river biota; however, no studies have examined the long-term effects of tributary inputs on fish population dynamics. This study examines nearly 40 years of young-of-year (yoy) paddlefish recruitment data to investigate the hypothesis that tributaries influence mainstem fish population dynamics. We generated hydrological variables from daily mean flow data (1965–2007) from an impounded reach of the mainstem Missouri River and from the Niobrara River, a relatively unaltered tributary, using Indicators of Hydrologic Alteration software. Three multiple regression models using natural-log transformed catch per unit effort (log cpue) as the response variable were created using (1) Missouri River-only flow variables, (2) Niobrara River-only flow variables and (3) Missouri River and Niobrara River flow variables. Flow variables from the Niobrara River explain a greater proportion of yoy paddlefish log cpue variability demonstrating that tributaries can positively impact fish population dynamics in altered rivers.