Bivalves have been extensively used to monitor aquatic habitats because their sedentary filter feeding habit results in the accumulation of elements from the environment. The genus Mytella is of special interest because its habit of burrowing in sediments can provide information about the substrate conditions in estuaries. Gill filaments have a large surface that is in constant contact with the water and therefore are used to monitor aquatic environments. In this study, we used scanning electron microscopy (SEM) to investigate the morphology of Mytella falcata gill filaments and to compare the gill structure in specimens from three sites (A, B and C) of the Santos estuary in southeastern Brazil. Site A presents low levels of pollutants, whereas sites C and B were directly affected by industrial discharges and harbor pollutants. The gill filaments of M. falcata have three types of cilia, namely, lateral cilia, eu-latero-frontal cirri and frontal cilia. Structures joining the inner and outer lamellae were found on the abfrontal surface, in addition to the presence of composite and simple cilia. A comparison of the filaments of bivalves from the three sites revealed no morphological alterations, but there was an accumulation of mucus on the frontal surface of the gill filaments of specimens collected at site B. This mucus may function as a protective barrier against pollutants. Bivalves from site C showed no such alteration, even though this site had the highest levels of pollutants. This lack of alterations may reflect the fact that these specimens were collected from concrete pillars where there would be less contact with pollutants. Our findings may reflect a long-term adaptation of these mollusks to chronic exposure to pollutants.