Shallow dynamic flows are very important processes in environmental systems, yet they are notoriously difficult to measure. For example, on coral reefs, shallow flows over the reef crest typically range from 0 to 1 m depth and velocity up to 1–2 m s−1 including oscillatory motion of waves. To directly measure depth and velocity in this challenging environment, we retrofitted a vertical acoustic Doppler current profiler (ADCP, Teledyne, RDI) designed for streams into a new shallow water acoustic Doppler current profiler system (SW‐ADCP) to expand memory and power limitations and allow for deployment in wave‐dominated environments. We captured variations in shallow reef crest depth and flow over a period of 3 weeks in the reef/lagoon system of Ofu Island, American Samoa. The new SW‐ADCPs recorded water depth and three‐dimensional velocity in 3 cm bins every 3 s. We then used velocity profiles to estimate volumetric flow and drag coefficients and verified these estimates using boundary layer theory. We observe that the mean velocity profile is well approximated by a log‐layer formulation with z0 of 3.5 cm, despite the shallow depths, strong flows, and breaking waves. Our observations validated the use of SW‐ADCPs as a tool for measuring flows in shallow (0.1–1 m), dynamic coastal marine environments.