The Missouri River in South Dakota was dammed in the 1950s and 1960s, altering the biotic and abiotic factors that potentially affect native species in the mainstem reservoirs. Little research has been conducted regarding what factors regulate age-0 CPUE (catch per unit effort) of native fish species since the damming occurred. Thus, we examined age-0 CPUE for thirteen native fish species in the four Missouri River mainstem reservoirs. We analyzed data from 1995-2015 in Lake Oahe, 2002-2016 in Lake Sharpe, 1998-2008 in Lake Francis Case, and 2000-2013 in Lewis and Clark Lake. Not all species were sampled in all reservoirs. We evaluated potential environmental (inflow, gauge height, peak flow, precipitation, air temperature) and biological (CPUE of other native species, non-native CPUE, predator CPUE) factors that have documented impacts on age-0 native fish CPUE. Significant relationships existed between age-0 native fish CPUE and both biotic and abiotic factors in all four reservoirs, but specific factors related to native fish CPUE were species and reservoir dependent. For all species examined in all reservoirs except age-0 Emerald Shiner Notropis atherinoides CPUE in Lewis and Clark Lake, age-0 CPUE was either stable or increasing. Age-0 Emerald Shiner CPUE in Lewis and Clark Lake was most supported by total age-0 non-native CPUE and adult White Bass Morone chrysops CPUE, and a positive relationship existed between age-0 Emerald Shiner CPUE and both factors. We believe our findings provide valuable insight into successful management of native fish populations.

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