Similar to most countries, the Brazilian water resources management considers topographically delineated catchment as a territorial unit for policy implementation. Yet, previous studies have shown that catchments are not hydrologically isolated, and topographic limits often neglect the groundwater boundaries. Thus, studies on effective catchment area are promising for shedding light on inter-catchment groundwater flow. Here, we investigated the deviation between the topographic and effective areas across Brazil. We applied the Effective Catchment Area index (ECI) to 733 Brazilian catchments and identified the most influencing attributes on the ECI by using Principal Component and Random Forest Analyses (PCA and RFA, respectively). Further analysis of consistency was carried out by contrasting the ECI values against the expected range of the Budyko curve considering both topographic and effective catchment areas (classic and adjusted framework). Considering the studied catchments, 15% and 16% of their effective areas were respectively smaller than half (strong losing water condition) and larger than double (strong gaining water condition) of their corresponding topographic areas. The aridity index was the main driving factor and negatively correlated with ECI followed by mean slope, precipitation seasonality, and mean elevation. In general, the more arid biomes in Brazil — the Cerrado and Caatinga — are prone to have smaller effective areas while larger effective areas were mostly found in the Atlantic Forest biome, a humid tropical region with a higher mean elevation. We highlight the potential of adopting a pooling of catchments based on their interconnectivity to minimize management costs while maximizing synergies and lessening trade-offs of water transfer processes. Our results contribute to a better country-scale understanding of hydrological connectivity among catchments and highlight the need to consider the effective catchment area to overcome water-food-energy security challenges on multiple scales.