Accurate demographic data play a critical role in implementing conservation strategies and identifying key areas for species preservation. The population abundance and density of Sotalia guianensis were estimated in the estuarine-lagoon complex of Cananéia, Brazil, using distance sampling. The survey covered 1339.91 km with 83 h 05 min in effort. A half-normal model with cosine adjustments was evaluated as the best fit to estimate an abundance of 193 individuals (95% CI 158–237) and a density of 2.55 ind km−2. The majority of sightings occurred in the Baía de Trapandé (48.72%), followed by the Mar de Cananéia (32.72%) and Mar de Cubatão (18.56%), the three areas surrounding the Ilha de Cananéia. The study confirmed the heterogeneous distribution of the estuary and found that the Mar de Cananéia and the Baía de Trapandé were more densely populated, with 2.76 ind km−2 (95% CI 1.93–3.96) and 2.76 ind km−2 (95% CI 2.07–3.66), respectively, while the Mar de Cubatão was less densely populated, with 1.59 ind km−2 (95% CI 1.04–2.44). The findings support previous research indicating a stable population over the last few decades. The Cananéia estuary is an ecologically diverse region located between protected areas under different categories of environmental protection and harbours a significant population of S. guianensis, providing essential resources for feeding and breeding. Protected areas have proven to be effective tools for preserving both marine and terrestrial environments. Despite the close proximity to humans and constant threats, the study underscores the importance of the area for the conservation of the species.