The aim of this study was to assess potential impacts of water quality changes associated with floods on the occupancy of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in two subtropical estuaries in Australia. Boat-based surveys were conducted in the Clarence River estuary (CR) and Richmond River estuaries (RR) over 3 yr. Principal components analysis (PCA) showed that when the dolphins were absent from the estuaries, three water quality components were extracted in the CR and two components in the RR. The PCA1 component included high loadings for salinity, turbidity, and pH for the CR (46%); and salinity, turbidity, pH, and dissolved oxygen (DO) for the RR (51%). Randomization tests showed that dolphins abandoned both estuaries at times of lower salinity, and during periods of higher turbidity and of lower levels of pH and dissolved oxygen in the RR that were associated with floods. The time until dolphins returned to the estuary postflood depended on the length and severity of the flood, but generally dolphins were observed in waters with salinity levels above 29‰. Their delayed return postflood could be for their physiological health, or because their prey returned to the estuaries under these higher salinity conditions, or more likely a combination of both factors.