Tributyltin (TBT) and Water-Soluble Fraction (WSF) of crude oil are usually present in estuarine coastal waters. The transport of rhodamine B by multixenobiotic resistance (MXR) mechanism and Scanning Electron Microscopy (SEM) analysis were used for the experimental evaluation of the individual and associated sublethal effects of TBT and WSF on the gills of Perna perna. The combined effects of WSF and TBT were studied. A set of experiments consisted in testing 25ng TBT/L and different WSF concentrations, whereas another set consisted in assays with 33% WSF and different TBT concentrations. The results showed an inhibition in the MXR transport activity of mussels exposed to 75 and 100% of WSF, while the concentration upper than 300 ng TBT/L induced the same mechanism. The results showed that TBT increases the effect of WSF when they are exposed together. Morphological analysis showed gills lesions only in the group of WSF. The observed disturbs were due to the organization of cilia on the surface of the lamellae with potential consequence to feed and gas exchange.