Salmo salar (Atlantic Salmon) smolts are exposed to predation pressure as they migrate from freshwater into the estuary and near-shore marine environment. In particular, Phalacrocorax auritus (Double-crested Cormorants) are a predator of Atlantic salmon smolts during their estuary and near-shore migration. National Oceanic and Atmospheric Administration's (NOAA) National Marine Fisheries Services’ (NMFS) telemetry data collected prior to this study (1997–2003), suggest that smolts are being removed from the Narraguagus River on their downstream out-migration. This removal may be the result of Cormorant predation. We investigated whether smolt survival could be improved by disrupting normal Cormorant foraging activity by integrating passive smolt tracking and active harassment techniques. Smolt movement and usage of various portions of the estuary according to light condition and tidal stage were explored along with concurrent avian harassment. Although harassment only occurred in approximately 33% of available daylight hours during this study, the impacts were easily recognized. Non-lethal harassment effectively displaced Cormorants from feeding locations and reduced loss of emigrating smolts. In 2004, 83.3% (15 of 18) of all smolt mortalities occurred on days of non-harassment, compared to only 16.7% (3 of 18) on days when harassment occurred. Similarly in 2005, 87.5% (7 of 8) of all smolt mortalities occurred on days of non-harassment, compared to only 12.5% (1 of 8) on days when harassment occurred. Non-lethal harassment appeared to be an effective means to reduce loss of emigrating smolts in the Narraguagus River estuary.