<p>Freshwater inflow is critical to the functioning of estuarine ecosystems but can have deleterious effects when large pulses reduce salinity below optimal levels for aquatic resident species. As climate change and anthropogenic interference with freshwater inflow intensify, fluctuations in estuarine salinity are expected to become more frequent and severe. Here, we use passive acoustics to capture a near-continuous, system-wide community response to a series of acute freshwater inflows into a large, dynamic estuary in South Texas. Our findings show decreased sonic activity across marine mammals, fishes, and invertebrates following the disturbance, effectively silencing the bay closest to the river mouths for several months. Sound production is critical for locating and capturing prey, courtship, and spawning for many estuarine species, suggesting that the suspension of sonic activity represents a notable interruption to ecosystem functioning, with potential long-lasting consequences for local stakeholders. Estuaries in semi-arid regions are expected to experience longer droughts broken up by more frequent severe flooding events during the coming decades. The ecological effects of these disturbances will be compounded by management decisions related to the extraction of freshwater resources, challenging managers to balance the needs of tightly intertwined ecological communities and coastal societies.</p>