Floodplain water flows have large volumetric flowrates and high complexity in space and time that are difficult to understand using water level gauges. We here analyze the spatial and temporal fluctuations of surface water flows in the floodplain of the Atrato River, Colombia, in order to evaluate their hydrological connectivity. The basin is one of the rainiest areas of the world with wetland ecosystems threatened by the expansion of agriculture and mining activities. We used 16 Differential Interferometric Synthetic Aperture Radars (DInSAR) phase observations from the ALOS-PALSAR L-band instrument acquired between 2008–2010 to characterize the flow of surface water. We were able to observe water level change in vegetated wetland areas and identify flooding patterns. In the lower basin, flow patterns are conditioned by fluctuations in the levels of the main river channel, whereas in the middle basin, topography and superficial channels strongly influence the flow and connectivity. We found that the variations in water level in a station on the main channel 87 km upstream explained more than 56% of the variations in water level in the floodplain. This result shows that, despite current expansion of agriculture and mining activities, there remain significant hydrological connectivity between wetlands and the Atrato River. This study demonstrates the use of DInSAR for a spatially comprehensive monitoring of the Atrato River basin hydrology. For the first time, we identified the spatiotemporal patterns of surface water flow of the region. We recommend these observations serve as a baseline to monitor the potential impact of ongoing human activities on surface water flows across the Atrato River basin.