Marine apex predators, such as coastal dolphins, are key components of ecosystem function and dynamics; understanding their spatial use therefore is important for conservation planning. Here, we describe spatial use of the threatened Guiana dolphin, Sotalia guianensis, within a mosaic of protected areas at their southern range in the Paranaguá estuarine complex (PEC), Brazil. Based on environmental characteristics and S. guianensis population densities, individual photo-identification surveys were focused on two sectors of the northern mouth of the PEC between 2013 and 2015. We photo-identified 107 individuals and recorded 351 groups of Guiana dolphins; nearly 50% of which contained calves. Group sizes were small (mean ± SD: Sector 1 = 3.4 ± 2.7; Sector 2 = 3.6 ± 2.0) and ranged from 1 to 30 individuals. Clustering algorithms were applied to resighted, photo-identified Guiana dolphins to classify individuals as “residents” (sighted in 87% of surveys, n = 11) and “transients” (two clusters; 62%, n = 22; 95%, n = 72). All individuals predominantly were observed foraging (90% in Sector 1 and 76% in Sector 2), but spatial use by transient individuals differed from the residents in terms of environmental (slope, water depth, and rainfall) and behavioral factors (presence of calves and foraging behavior). Compared to transients, resident dolphins ranged over smaller areas, typically more suitable for feeding, calf caring, and more protected from predators and vessels. Because resident Guiana dolphins exhibit small home ranges, they are particularly vulnerable to local anthropogenic activities and habitat loss. These characteristics imply a strong need for regionalized management plans to reduce negative impacts and to maintain the ecological functionality of the species.