Beaked whales are cryptic and difficult to study species, often distributed in deep offshore waters and only briefly visible at the surface. A diverse range of cetacean species has been documented in the Bay of Biscay, including several species of beaked whales. However, little is known about how persistent their presence is. Citizen science data collected during ferry-based surveys between 2006 and 2018 were analysed to investigate how encounter rates varied across space and time, and their drivers for beaked whale species. Approximately 244,400 km were surveyed, and there were 419 encounters with beaked whales recorded including Cuvier’s beaked whales, (n = 260), Northern bottlenose whales (n = 19), Sowerby’s beaked whales (n = 13), and True’s beaked whales (n = 1). Generalized Additive Models revealed that encounters were generally more frequent in the southern bay, on northern facing slopes, with all species except Sowerby’s showing a preference for both deep waters and shallow shelf waters. Animals were recorded in each of the eight surveyed months, suggesting that beaked whales may be present year-round, with increased encounter rates in summer months. This study is the first to indicate that beaked whales may persist in this area throughout the year, which is key information for appropriate management.