Ectotherms in water experience rates of heat transfer at least two orders of magnitude greater than in air, seriously constraining their thermoregulatory capabilities. Yet, even in water, individuals may exert control over body temperature (T b ) via behaviors such as selecting thermally favorable microhabitats. The interactions among body size, physiology, and behavior on the thermal biology of large, entirely aquatic, ectotherms is poorly understood. We tested the hypothesis that alligator snapping turtles (Macroclemmys temminckii) selected microhabitats based on temperature by comparing temperatures at sites used by turtles to temperatures at randomly selected sites. These large turtles selected a narrow range of microhabitats that were significantly warmer and less variable in temperature than random sites. Cooling trials in the laboratory indicated larger turtles equilibrated more slowly to ambient temperature (T a ) than smaller turtles. We recorded T a and body temperature (T b ) of turtles in the field continuously throughout the year. The T b generally conformed to T a but there were periods when T b −T a differences were great. These results suggest that while physiology and size of aquatic turtles can affect T b transiently, microhabitat selection may be the only meaningful mechanism for large, entirely aquatic, turtles to control T b .