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We studied 24 wetlands along a 296‐km portion of the lower Missouri River floodplain, USA during 1996–1998. Our goal was to examine relationships between wetland characters and freshwater turtle diversity. We collected data on a total of 2201 individual captures of six freshwater turtle species. Ten species variables (richness, evenness, proportion of lentic species combined, proportion of lotic species combined, and proportions of six individual species) described the turtle assemblage structure and were associated with six broad wetland categories (remnant oxbow, remnant slough, connected scour, isolated scour, temporary farmed, and temporary not farmed) as well as with six abiotic (water depth, distance from the river, duration dry, duration flooded, size, and turbidity) and two biotic (primary and secondary productivity) wetland characters. Repeated‐measures MANOVA and ANOVA revealed highest diversity in remnant sloughs and oxbows as well as in newly created scour wetlands and lowest diversity in temporary wetlands. Multiple regressions and correlations indicated that the single most important wetland characteristic for high turtle diversity was a low annual duration of drying. Oxbows supported the highest proportions of lentic turtles; while connected scours supported the highest proportions of lentic turtles. Lentic species proportions were highest in wetlands that were frequently flooded, relatively distant from the Missouri River, and insect rich, while lotic species proportions were highest in wetlands that were turbid, close to the river, and relatively insect poor. The cohabitation patterns of several turtle species suggest that direct or indirect interactions between species may affect assemblage structure. Based on our broad array of wetlands, we identified crucial wetland types and characteristics that were associated with maximum diversity for freshwater turtles. Empirical studies similar to ours across broad landscapes are needed for a variety of wetland floral and faunal groups before sound conservation and management recommendations can be formulated.