In this study we describe how franciscana and Guiana dolphin habitat use is influenced by tidal cycles and seasonality in Babitonga Bay. The franciscanas use a greater area in winter and a smaller area in summer, but the extent of the area used did not vary with the tide. Guiana dolphins did not change the extent of the area used within seasons or tides. Franciscanas remained closer to the mouth of the bay and the islands during ebb tide, moving to the inner bay areas and closer to the mainland coast during flood tide. Guiana dolphin used areas closer to the mainland coast during the flood tide. Guiana dolphin patterns of movement do not seem to be related to the tidal current. Franciscanas used sandier areas while Guiana dolphins preferred muddy areas, with some seasonal variation. We suggest that these dolphins modify their distributions based on habitat accessibility and prey availability. This study enhances our knowledge of critical habitat characteristics for franciscana and Guiana dolphins, and these factors should be considered when planning local human activities targeting species conservation.