Understanding how community compositions are affected by environmental and spatial factors are essential to provide knowledge about the distributions of species. Furthermore, these factors can play a role in species morphological variation. Tadpoles can be found in different types of aquatic microhabitats, showing a considerable amount of morphological diversity. We hypothesized that tadpole morphological diversity is controlled by ecological and spatial factors other than assemblage attributes, and that tadpole assemblage composition is affected by spatial factors. To test these hypotheses, we recorded the abundance of tadpoles from different ponds, identified eight environmental variables that represented local and landscape descriptors of the ponds, recorded the spatial coordinates of the ponds, and measured the morphological variation of assemblages. Spatial factors significantly affected the composition of tadpole assemblages, while both spatial and environmental factors affected morphological variation. The ability of tadpoles to alter their morphology in response to environmental factors might be a result of poor oviposition site choice, and this probably interacts with spatial factors to control the assemblage composition of tadpoles. Morphological variation is advantageous for tadpoles because it allows them to adjust their morphology to environmental conditions. This study has demonstrated how factors that control the assemblage composition of tadpoles also drive their morphological diversity.