Understanding how multiple species and populations vary in their recruitment dynamics can elucidate the processes driving recruitment across space and time. Lake Whitefish (Coregonus clupeaformis) and Cisco (C. artedi) are socioecologically important fishes across their range; however, many Laurentian Great Lakes populations have experienced declining, poor, or sporadic recruitment in recent decades. We integrated catch and age data from 38 long-term surveys across each of the Great Lakes and Lake Simcoe, resulting in a combined time series spanning 1960–2019. We estimated Lake Whitefish and Cisco year-class strength (YCS) in each lake using longitudinal mixed-effects regressions of relative cohort abundance. We subsequently quantified interspecific, spatial, and temporal synchrony in YCS using correlation and dynamic factor analyses. Lake Whitefish YCS was positively spatially synchronous on average, and YCS in all six lakes was elevated during the 1980s–1990s. In contrast, Cisco YCS was sporadic, not spatially synchronous, and highly variable around long-term, lake-specific means. YCS was not synchronous between species in any lake. Collectively, our analyses demonstrate that these species exhibit differential recruitment dynamics that may be regulated by species-specific factors. Results from this study can be leveraged in future research on the causes and consequences of cross-species, cross-basin recruitment variability.