We tested if there was a difference in mass-specific excretion rate between two genetically size-divergent brook trout (Salvelinus fontinalis) populations that can be accounted for by genetic/maternal factors. We conducted laboratory-based common garden experimentation using F1 generation fish, with five to seven families per population at two ages (0.5 year juveniles and 1.5 years adults). We found that genetic/maternal differences in excretion rate on a per gram basis coevolve with genetic divergence in adult body mass between the populations. However, this coevolution has also resulted in no net difference in excretion rate between populations when differences in adult body mass were accounted for. Uncertainty in census estimates and variation in body mass distributions created substantial variation in extrapolated whole-population excretion estimates. No other studies to our knowledge have tested for genetic/maternal divergence in excretion rate between genetically size-divergent fish populations. Genetically based population divergence in body mass, energy allocation in reproduction, and mass-specific excretion rate in the brook trout was likely a result of selection associated with differences in the availability of overwintering habitat between streams.