The exquisite transitional fossil Tetrapodophis – described as a stem-snake with four small legs from the Lower Cretaceous of Brazil – has been widely considered a burrowing animal, consistent with recent studies arguing that snakes had fossorial ancestors. We reevaluate the ecomorphology of this important taxon using a multivariate morphometric analysis and a reexamination of the limb anatomy. Our analysis shows that the body proportions are unusual and similar to both burrowing and surface-active squamates. We also show that it exhibits striking and compelling features of limb anatomy, including enlarged first metapodials and reduced tarsal/carpal ossification – that conversely are highly suggestive of aquatic habits, and are found in marine squamates. The morphology and inferred ecology of Tetrapodophis therefore does not clearly favour fossorial over aquatic origins of snakes.