Pollutants found dispersed in water can cause irritations on the gills, challenge the immune system and prejudice the welfare of the fish. Here we investigated molecules linked to proliferation, survival, and cell death, as well as inflammatory and vascular control, in a model of fish gill remodeling, from injury to recovery. We assessed the gill histology and immunohistochemistry for PCNA, iNOS, HSP70, and Bax in Hypostomus francisci obtained from a river subjected to chronic anthropic influences and then after they were placed in water of good quality. A total of 30 H. francisci adult individuals were collected and distributed into two groups: euthanized on the day of capture (group 1) and maintained for 30 days in an aquarium (group 2). In all the fish from group 1, the primary and secondary lamellae showed hypertrophy of the respiratory epithelium, lamellar fusion, lifting of the epithelium, aneurysm, hyperemia, and vascular congestion. On the other hand, in all the fish from group 2, restoration of gill integrity was observed, and the primary and secondary lamellae showed a simple epithelium, absence of lamellar fusion, hypertrophy, and aneurysm. Gills of fish from group 1 had higher frequency of cells immunopositive for PCNA, iNOS, HSP70, and Bax than those of fish from group 2 (p < 0.05). The molecular and cellular mechanisms from injury to recovery were proposed, with a balance between survival and cell death signals being essential for determining the gill structure. In addition, the findings indicate that recovery of the structural organization of gills is possible if fishes are maintained in good-quality water, indicating the importance of the conservation of aquatic environments.