Dam-controlled river stage fluctuations alter groundwater–surface water interaction between persistent bars and islands and the rivers bounding them by rapidly changing hydraulic gradients and expanding hyporheic zones. A 300-m long and 80-m wide sand-gravel island with established vegetation located on the Colorado River (Austin, Texas, USA) is subjected to >1 m daily river stage variations due to upstream dam operations. Piezometer nests with probes monitored the evolution of the water table and groundwater flow paths through several cycles of dam-induced stage fluctuations. Results show that hydraulic head and the water table within the island closely track the river stage associated with dam release. Water table mounds and depressions which overlap in time were mapped through the course of one storage-release cycle over which >4,000 m3 of water moved in and out of the island. Dam operations have drastically altered groundwater–surface water connectivity between the Colorado River and the fluvial island aquifer by pumping substantial amounts of water in and out of the aquifer during dam release and storage cycles.