If the flow is oscillating, the best approach is to collect enough transects that you capture the full range of the change one or more times depending on the duration of the change. You can then decide in post processing if you want to average transects that cover the full range for one cycle to get an overall average, or average fewer (maybe use individual transects) to define the full range and clearly show the cyclic nature of the flow. Collecting many transects and then using individual transects or an average of just a few at a time is commonly done to characterize flow in tidal environments. In your situation, the key is to collect enough transects to fully characterize the flow changes.
Dave