AbstractLarge‐scale aquatic mesocosm studies were formerly required by the U.S. Environmental Protection Agency (EPA) for ecological risk assessment in pesticide registration. However, the use of bluegill sunfish (Lepomis macrochirus Rafinesque) to evaluate pesticide effects on fish reproduction in large mesocosms (>300 m3) resulted in over‐exploitation of invertebrates by large numbers of young‐of‐the‐year (YOY) bluegill, thus confounding the interpretation of pesticide effects. As an alternative, a reproduction study with fathead minnows (Pimephales promelas Rafinesque) was conducted in 17‐m3 outdoor microcosms. The objective of this research was to evaluate the effects of varying sex ratios of 20 adult fathead minnows (FHMs) on their reproduction during a 4.5‐month period. The outcome of this study was compared to a bluegill reproduction study in 400‐m3 mesocosms conducted synchronously. The logistics of monitoring the microcosms were simpler, and harvesting FHMs from microcosms took considerably less effort in comparison to harvesting bluegills from mesocosms. The FHMs produced a smaller number of larger young in comparison to bluegills, which produced large numbers of less mature YOY. The variability in total fish biomass between replicates was greater in the bluegill study, resulting in less statistical power to detect biomass effects. The FHM sex ratios significantly affected reproduction and growth, thus altering the fish population structure, despite similar stocking densities. Sex ratios with similar numbers of males and females produced a lower total biomass and number of YOY. There was no evidence of system carrying‐capacity constraints on FHM growth or reproduction.