Substantial mortality can occur in age-0 fish populations during their first year of life, especially in winter; this can potentially influence overall recruitment into the adult population. As such, we compared relative abundances between fall and spring catches of sympatric juvenile bluegill Lepomis macrochirus Rafinesque and yellow perch Perca flavescens (Mitchill) to evaluate the magnitude of overwinter mortality across locations (five lakes for two years) and through time (one lake for six years). In addition, we compared both quantile-quantile and increment plots, based on length-frequency histograms from fall-and spring-caught cohorts from 2004 to 2010, to determine if mortality was sizeselective while accounting for over winter growth. Bluegill relative abundances (as indexed by catch-per-unit-effort) significantly decreased from fall to spring, although size-selective mortality was not detected in 10 instances. Yellow perch relative abundances were similar from fall to spring in five Nebraska Sandhill lakes; however, size-selective mortality was detected, with size-selective over winter mortality of smaller individuals occurring in one of eight instances, whereas greater mortality in larger individuals occurred in two instances. Positive growth occurred in both species but was variable among lakes and appeared to be system-specific. In Nebraska Sandhill lakes, over winter mortality likely differs between these two species in its severity, size-selective effect, and scale (i.e., lake-specific vs. large-scale processes), and is likely influenced by combinations of these (and potentially other) factors.