ABSTRACT: Franciscana dolphins in Babitonga Bay represent the only fully estuarine population of this critically endangered species, but this location is also home to a population of Guiana dolphins. Surrounded by large cities and harbors, Babitonga Bay presents intense human activities and potential impacts that may threaten the dolphins. Understanding their habitat use and distribution can inform the implementation of conservation actions and mitigation of such impacts. Here, we used acoustic data from 60 fixed passive acoustic monitoring stations, implemented between June and December 2018. The relationship between the occurrence of franciscanas and environmental variables was investigated with generalized additive mixed models. The selected model presented 51% of explained deviance and included time of day, intensity of presence of Guiana dolphins, maximum slope, and bottom sediment, among other less statistically significant variables. A daily distribution pattern was identified, with franciscanas remaining in the areas of greatest occurrence especially in the morning and seeming to prefer sandy bottom and flatter areas. Areas intensively used by Guiana dolphins were avoided. Additionally, we mapped their distribution using empirical Bayesian kriging to identify the main areas of occurrence and for foraging. Franciscanas are consistently predominant in the innermost region of the estuary, without expressive use of the entrance channel, but with a wider range in winter than in spring. The area around the islands, between the north and south banks, represents an important foraging area, a behavior more frequent during dawn and night. This study provides important insights into critical habitats and behavioral patterns of critically endangered franciscanas in Babitonga Bay.