The Matusagaratí wetland in the Panamanian Darien is one of the largest wetlands in Central America. These types of riverine wetlands, associated with large drainage basins, are complex hydrological environments where variations in water flows and exchanges condition the existence of different wetland habitats. The work aimed to establish the hydrological functioning of the Matusagaratí wetland in different sectors of the Balsas River, emphasizing the exchanges of surface and groundwater flows and the hydrological connectivity that exists between the different laterally linked wetland environments. For this purpose, a monitoring network for surface water and groundwater was established along transects intersecting various wetland environments in the middle and lower basin of the Balsas River. This network is complemented by measurement points for surface water located in streams and in the upper basin of the river. Data collected in sensors installed in boreholes were compared to river level and precipitation data. Continuous water level recording sensors were installed at the monitoring points, and samples were collected for the determination of major ions and stable isotopes. The results indicate that in the mangroves of the lower basin and in the cativo forests of the middle basin levee there is a strong exchange of water between the river and the shallow groundwater. This water exchange is strongly influenced by the tide which spreads from the estuary to the continent through the river. Meanwhile, in the middle basin, mixed forests and orey forests developed on the alluvial plain exhibit a hydrological functioning that depends primarily on precipitation inputs. This study provides data that could serve as a basis for the management of this large tropical wetland that, despite having protection initiatives, could be hydrologically impacted by unsustainable socio-economic practices.