Rivers are amongst the most endangered systems in the world. They suffer a multitude of pressures that act at various temporal and spatial scales. Longitudinal connectivity reduction is one of the most severe impacts forced upon river networks. Transversal barriers, such as dams, break up the original network into several sub-networks, promoting species and populations’ isolation by limiting fish movements which might lead to genetic bottlenecks and loss of populations. These impacts exist worldwide and there is a need for numerical tools that help to understand the extent of the impacts and facilitate correct allocation of resources for restoration actions. Thus, this work aims at measuring the impact of connectivity reduction on the distribution of freshwater fish species and to quantify overall river network connectivity. To achieve these objectives several habitat suitability modeling techniques and a spatial graph approach were employed. We were able to assess the impact of barriers placement on the structural and functional connectivity of river networks - using both resident and migratory fish species; and also to develop a technique that allows the overall connectivity of a given network to be quantified. This technique is further useful to aid decision-making by prioritizing barriers to intervene and enhance connectivity and to determine where to place new instream barriers reducing overall connectivity impacts.