Abstract Biogeographical patterns explain variation in body size, although the strength and directions of these patterns vary. When researchers account for the micro- or macrohabitats that species inhabit, they often find that biogeographical relationships with body size are modified, especially in taxa that inhabit diverse environments. Freshwater crayfishes are an ideal group in which to study the interaction between habitat, biogeography, and body size, because there are >700 crayfishes that inhabit aquatic environments, semi-terrestrial burrows, and caves. Here, we explore evolution of body size across 452 species of crayfish by considering the interaction between their habitats (aquatic, semi-terrestrial/aquatic, semi-terrestrial, and cave-dwelling) and the mean temperature of their geographical range. We documented 64-fold variation in body length. Aquatic species were the largest and had the greatest variation in body size. Crayfishes that inhabit both semi-terrestrial and aquatic habitats exhibit a weak negative relationship between body size and environmental temperature; solely aquatic species reverse this relationship. Evolutionarily, our ancestral reconstruction suggests that the ancestral crayfish was an aquatic species with a body length of 81.1 mm, which aligns with data from fossil crayfish. Overall, our study highlights how uniting biogeographical and evolutionary approaches improves our ability to explore patterns of animal body size and unearth explanatory mechanisms.