Tadpoles have been classified into ecomorphological guilds according to their general morphology, feeding behavior, and ecology. Individuals of benthic and nektonic ecomorphological guilds have distinguished morphological traits, but they can also adapt their morphology in response to environmental changes through phenotypic plasticity. We hypothesized that the degree of morphological variation in response to environmental changes would not be equal for different guilds. We predicted a high correlation between morphology and environmental variation for benthic tadpoles, while the morphology of nektonic and intermediate benthic-nektonic tadpoles would be less correlated with environmental variation. We sampled 32 ponds, collected 109 individuals from three species (Boana albopunctata, Dendropsophus minutus, and Scinax fuscomarginatus) and measured five environmental variables for each pond. We used the geometric morphometric approach to describe the morphological variation of tadpoles and a redundancy analysis (RDA) to assess the relationship between the morphological variation of tadpoles and environmental traits for each ecomorphological guild. We detected a phenotype-environment association only for the nektonic tadpole (Dendropsophus minutus). We suggest that tadpoles from different ecomorphological guilds were exposed to different levels of environmental heterogeneity, but benthic and intermediate benthic-nektonic tadpoles actively selected the pond patches that maximized their efficiency, showing less correlation with environmental changes Conversely, nektonic tadpoles were subjected to higher environmental heterogeneity associated with the substrate of the ponds, vegetation, and land use around the pond perimeter, which resulted in higher morphological plasticity.