Since marine ecosystems provide vital services for humans, the United Nations established the goal to “Conserve and sustainably use the oceans, seas and marine resources for sustainable development” through the 2030 Agenda. This goal induces the establishment of a network of Marine Protected Areas (MPAs) and proposing tools to manage marine resources in sustainable ways. In particular, the Aichi Targets indicate that, until 2020, each country should protect at least 10% of coastal and marine areas, especially those important for biodiversity maintenance and ecosystem services. Although Brazil has recently reached 25% coverage, studies revealed the ineffectiveness of some MPAs. Therefore, to evaluate the effectiveness of MPAs, we chose two of the largest Guiana dolphin populations (Sotalia guianensis) as bioindicators. Dolphins comprise good indicators of ecosystem health, acting as key, umbrella, sentinel and top predator species, being sensitive to human disturbance. Since these populations are in two areas considered a priority for the conservation in Brazil (Sepetiba and Ilha Grande bays), the effective protection of their areas will likely safeguard several other marine species, such as fishes, seabirds and invertebrates.