New wind sensing technologies are needed to measure atmospheric flows in aquatic environments where hazardous agents may be present and conventional atmospheric sensors are difficult to deploy. Here, we present the application of model-based multirotor sUAS (small uncrewed aircraft system) wind estimation to measure atmospheric flow variations in aquatic environments. Thirty-two sUAS flights were conducted at Grand Lake St. Marys (GLSM), Ohio in August, 2019 to characterize differences in wind profiles (wind speed and wind direction) across onshore and offshore (over the lake) locations 80 m apart. A harmful algal bloom was present in GLSM during the experiment. Fourteen calibration flights were conducted at the same site to validate multirotor sUAS wind estimates hovering next to a sonic anemometer (SA) installed 13 m above ground level. Forty-seven calibration profiles were performed in Blacksburg, Virginia on June 30th, 2020 to validate multirotor sUAS wind estimates obtained in steady ascending vertical flight next to a SoDAR wind profiler. Differences between onshore and offshore wind speed measurements at GLSM increased from morning to afternoon on each day of experiments. Flights performed next to SA and SoDAR instruments also demonstrated multirotor sUAS estimates of wind velocity components u and v to have mean absolute error values of 0.4 m s−1 and 0.3 m s−1 (hovering) and 1.2 m s−1 and 1.5 m s−1 (ascending), respectively. Overall, our findings support further development of multirotor sUAS capabilities for resolving atmospheric flows in aquatic environments.