Devil's Slide Rock, a rock sea stack on the central California coast near San Francisco, USA, hosts a Common Murre (Uria aalge) colony that was recently restored after it was extirpated in the mid-1980s. Since the late 1990s, low-flying aircraft have threatened the colony at Devil's Slide Rock. To assess variables contributing to Common Murre disturbance, multinomial log-linear models were constructed and evaluated using reproductive timing and aircraft characteristics for 7 years (2008–2014). The top model included seven variables (year, reproductive timing, time of day, aircraft type, aircraft category, aircraft altitude and aircraft lateral distance from Devil's Slide Rock) and the interaction effects between aircraft type and aircraft category, and between altitude and distance. The odds of disturbance varied temporally, with 2010, 2011, 2013 and 2014 exhibiting greater odds of disturbance than 2008. Disturbance response was more likely during the pre-egg lay period and post-chick hatch period than during incubation; 47%, 51%, and 40% of over-flights, respectively, resulted in agitation or flushing. Helicopters were more likely to cause disturbance than fixed-wing aircraft; 72% of helicopter over-flights and 39% of fixed-wing aircraft resulted in agitation or flushing. Flushing was more likely to occur at lower aircraft altitudes and closer lateral distances; all flushing from over-flights occurred below 305 m, and 91% of agitation events occurred below 305 m. These results support the need for measures to reduce over-flight disturbance of the Devil's Slide Rock colony.