The human contribution to ambient noise in the ocean has increased over the past 50 years, and is dominated by low-frequency (LF) sound (frequencies <1000 Hz) from shipping, oil and gas development, defence-related and research activities. Mysticete whales, including six endangered species, may be at risk from this noise pollution because all species produce and probably perceive low-frequency sound. We conducted a manipulative field experiment to test the effects of loud, LF noise on foraging fin blue (B. musculus) and (Balaenoptera physalus) whales off San Nicolas Island, California. Naive observers used a combination of attached tracking devices, ship-based surveys, aerial surveys, photo-identification and passive monitoring of vocal behaviour to examine the behaviour and distribution of whales when a loud LF source (US Navy SURTASS LFA) was and was not transmitting. During transmission, 12-30% of the estimated received levels of LFA of whales in the study area exceeded 140 dB re 1 μPa. However, whales continued to be seen foraging in the region. Overall, whale encounter rates and diving behaviour appeared to be more strongly linked to changes in prey abundance associated with oceanographic parameters than to LF sound transmissions. In some cases, whale vocal behaviour was significantly different between experimental and non-experimental periods. However, these differences were not consistent and did not appear to be related to LF sound transmissions. At the spatial and temporal scales examined, we found no obvious responses of whales to a loud, anthropogenic, LF sound. We suggest that the cumulative effects of anthropogenic LF noise over larger temporal and spatial scales than examined here may be a more important consideration for management agencies.