The Minas Passage, one of the Bay of Fundy’s tidal channels, located in Nova Scotia, Canada, presents significant potential for tidal energy development because of its highly energetic flows. The rise of floating tidal turbines makes it increasingly important to develop tools for accurate spatiotemporal near-surface flow mapping in the area. In this investigation we present a strategy for minimizing boundary data loss from stationary, bottom mounted acoustic Doppler current profilers by implementing a sigma coordinate system. Historical records for acoustic Doppler current profiler deployments at the FORCE site in Minas Passage are examined. The acoustic time series are compared to harmonic reconstructions, which suggest that there is significant non-tidal behaviour at the water surface. Wind and turbulence are considered as possible explanations for these observations. Variance in the vertical beam of the acoustic Doppler current profiler is compared to time series of wind speed and direction. High wind events in directions opposing the principal flow are found to coincide with high variance in the vertical beam. This work is presented as the foundation for future work in Minas Passage, which will involve the integration of acoustic Doppler current profiler data with other technologies, including X-band marine radar, to map the complete water column.