Cetacean communities face significant threats from adverse interactions with human activities such as bycatch, vessel collision, and environmental pollution. Monitoring of marine mammal populations can help to assess and safeguard marine biodiversity for future generations. Traditional surveys can be costly and time-consuming to undertake, but we explore the ability of citizen science to inform environmental assessments and subsequent conservation management. We use data collected from platforms of opportunity within the Bay of Biscay to investigate spatial changes in cetacean diversity, with the aim of identifying hotspots which may be suitable for further investigation and conservation. Seventeen species of cetaceans were recorded over a ten year period, many of which are data deficient in European waters (e.g. Bottlenose dolphin, Short-beaked common dolphin, Striped dolphin, Risso's dolphin, Long-finned pilot whale, Killer whale, Northern bottlenose whale, Cuvier's beaked whale, Sowerby's beaked whale and True's beaked whale). Biodiversity (determined by Simpson's Diversity index) ranged from 0.19 to 0.77. The central and southern areas of the survey area indicated the highest biodiversity (0.65–0.77), and these locations may benefit most from protection as Important Marine Mammal Areas. We present a case for this designation, and discuss the benefits and limitations of citizen science for informing conservation action.