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Methods used in wildlife ecology can influence population‐ and community‐level estimates, such as species richness, sex ratio, age and size structure, occupancy and detection probabilities, and community composition. Various trapping and sampling biases exist for freshwater turtles including bait and trap choice and survey technique. To date, no study has investigated the influence of hoop net and mesh size on various population‐ and community‐level estimates. Here, we use detection models to determine if trap and mesh size influence detection probability of nine species of freshwater turtles over 3 consecutive years (2016–2018) in west Tennessee. Additionally, we use multivariate models to determine if freshwater turtle community composition was influenced by hoop trap and mesh sizes. Our results indicated that there was a bias related to mesh size in detection probabilities and community composition. Smaller mesh sized traps were better at detecting smaller‐bodied turtle species, which then changed community species richness but not catch‐per‐unit‐effort estimates (i.e., abundance). Additionally, larger mesh sized traps were better at detecting common snapping turtles (Chelydra serpentina), which supports previous research. Our results suggest that researchers should account for the variation in detection probabilities by mesh size when conducting mark‐recapture and occupancy analyses. Moreover, erroneous inferences about population trends and changes in diversity within turtle communities through time could cause managers to misidentify population declines and conservation value of a site. © 2021 The Wildlife Society.