Successful locomotion is essential for an animal’s survival and is the basis for an overwhelming number of vital behaviors an animal will perform throughout its life. The structural complexity of the natural world requires an organism to respond to environmental heterogeneity by fine-tuned kinematic adjustments of the musculoskeletal system. Understanding how animals adjust their performance in response to external perturbations by the substrate and external environment is essential to understanding what forces underlie the evolution of novel morphologies and locomotor strategies. Basilisks (Basiliscus spp.) are tropical lizards that are well-known for their remarkable ability to run across the surface of water. Although previous work within Basiliscus has investigated hind limb kinematics while running on still water, it is unclear how basilisks modulate their locomotor behavior when running across flowing water. Investigating the effects of flow on locomotor performance is highly relevant to the ecology of Basiliscus, as they are known to utilize both lentic (ponds, lakes, lagoons) and lotic (creeks, streams, rivers) habitats as part of their life history. We utilized three-dimensional high-speed video technology to capture water-running behaviors of Basiliscus plumifrons under three flow regimes: no-flow, medium-flow, and high-flow. B. plumifrons increases its stride frequency, running speed, and joint angular velocities at intermediate water velocities and begins stance with a more rotated femur across high-flow treatments. Additionally, the femur retracted less on flowing treatments than still water, and least on medium-flow conditions. The metatarsophalangeal joint (MTP) in the middle of swing was more flexed across high-flow velocities, suggesting the toes were in a more cupped position. Overall, hip height and duty factor exhibited little variation across all treatments. These results suggest that changes in the specific locomotor strategy of an organism can result in similar locomotor performance measures. The results of this study could provide insight into the selective forces directing the evolution of novel locomotor strategies and the response of organisms to complex environmental conditions and habitat alterations.