Recent advances in acoustic Doppler current profiler (ADCP) allow for measuring spatially continuous and high resolution hydraulic data such as water depth and flow velocity that are the basis for ecohydraulic analysis and modelling. In this paper, an ADCP and a conductivity-temperature-depth (CTD) profiler were used for depth measurement in Zuibaji river in Fukuoka, Japan, and accuracies of these measurements were assessed and compared based on tape-measured water depth with a GPS coordinate. As a result, water depth measured with a CTD profiler and an ADCP showed a good agreement with observation data, which supports the applicability of the ADCP and CTD for bathymetric survey. A major source of error seems to be a positioning error for obtaining GPS coordinates on site. Further study considering measurement errors, systematic errors and positioning errors, may be needed for a deeper understanding of error characteristics, leading to a better application of these innovative technologies for ecohydraulic surveys.