Recruitment of many fish populations is inherently highly variable inter-annually. However, this variability can be synchronous at broad geographic scales due to fish dispersal and climatic conditions. Herein, we investigated recruitment synchrony of Silver Carp Hypophthalmichthys molitrix across the Mississippi River basin. Year-class strength (YCS) and synchrony of nine populations (max linear distance = 806.4 km) was indexed using catch-curve residuals correlated between sites and related to local and regional climatic conditions. Overall, Silver Carp YCS was not synchronous among populations, suggesting local environmental factors are more important determinants of YCS than large-scale environmental factors. Variation in Silver Carp YCS was influenced by river base flow and discharge variability at each site, indicating that extended periods of static local discharge benefit YCS. Further, river discharge and air temperature were correlated and synchronized among sites, but only similarities in river discharge was correlated with Silver Carp population synchrony, indicating that similarities in discharge (i.e., major flood) among sites can positively synchronize Silver Carp YCS. The positive correlation between Silver Carp YCS and river discharge synchrony suggests that regional flood regimes are an important force determining the degree of population synchrony among Mississippi River Silver Carp populations.