Underwater features at shallow depth (∼ 40 cm) are difficult to be observed and monitored. The water surface disturbed by flow and wind action prevents the direct observation from above water. Water-proofed camera or video are also hard to maneuver in such situations. In this study, we tackle this problem by using continuous photos (∼2000 photos per site) taken from above water and setup on a tripod. We employed a Nikon D200 camera, which takes about 3 - 12 minutes for each site. A grey card of photogrammetric grade is used to adjust the temporal change of illumination condition. Test sites include two flow types, i.e., no perceptible flow and smooth. A mode-based filter scheme is developed to filter the pixels that are disturbed by wave actions. The results show that the proposed filter is most effective for both flow types, where the water surface is mostly flat.