Conservation biology has historically been based on principles to protect terrestrial ecosystems, with marine and freshwater ecosystems left behind. As a result, often, protected areas are defined with bases in forest cover and terrestrial characteristics overseeing important components of connectivity of riverine landscapes, such as the connectivity between rivers, lakes, and streams. It is important to emphasize that forest protection is extremely important, but that alone cannot safeguard the protection of freshwater ecosystems. Therefore, our discussion should lead, not to the disregard of terrestrial efforts but to the complementation of existing efforts for forest protection with the addition of areas that can also protect freshwater ecosystems. Fluvial ecosystems are hierarchical and nested systems, with multidimensional connectivity including longitudinal (upstream-downstream), lateral (floodplains and lakes), temporal (seasons) and vertical (groundwaters) connections. Systematic Conservation Planning (SCP) is the most well accepted and used method for designing conservation plans based on cost-effective scenarios that include ecological and socio-economic values resulting in thematic maps of priority areas for conservation. Recently, methods to consider the connectivity of freshwater ecosystems were incorporated into spatial prioritization tools. Maps produced using spatial prioritization tools can help decision making on species management and conservation actions, such as plans for species’ impact reduction (PRIM) and action plans for threatened species (PAN). PRIM and PAN use information about species ecology to focus conservation actions onto target species. These conservation action plans must be viable not only ecologically but also economically. In this context, using SCP to guide designs of PRIM and PAN can help stakeholders to achieve better conservation actions in Brazil. Thus, the SCP can improve the conservation and management of freshwater ecosystems, through the integration of science, society and stakeholder.