By using 6 years of Long Term Resource Monitoring Program (LTRMP) turtle by-catch data collected from the middle Mississippi River, we investigated smooth softshell (Apalone mutica) and spiny softshell (Apalone spinifera) turtle abundance collected from 5 physical habitats: main channel border, wing dikes, tributary, open side channel, and closed side channel. Females comprised 62% and males 38% of the total catch of smooth softshell turtles. For spiny softshell turtles, females comprised 67% and males 33% of the total catch. We observed skewed reproductive age structure and sex ratios among and within both species. Smooth and spiny softshell turtle captures were dominated by reproductive individuals (62% and 87%, respectively). Smooth softshell turtles were most abundant in open side channels and main channel borders, whereas spiny softshell turtles were most abundant in tributaries and closed side channels. Smooth softshell abundance was greatest in deep waters with faster water velocity, whereas spiny softshell abundance was greatest in waters with higher visibility (e.g., Secchi transparency) and slower water velocity.