Regular monitoring of the status of cetacean populations is essential for conservation, policy and management. By using a passenger ferry as a scientific research platform, this study provides information on seasonal, annual and longer-term changes in the occurrence of three cetacean species along a relatively fixed transect through the English Channel and the Bay of Biscay. Data were collected over an 11 year period through the Biscay Dolphin Research Programme (BDRP). Surveys were conducted every month from 1996–2006 between Portsmouth, England and Bilbao, Spain by a team of experienced observers using standard techniques. From a 0.125° by 0.125° grid, cells were surveyed in each year and where each species was recorded they were identified using a geographical information system (GIS). A rapid analytical method—species occupancy (defined as the proportion of surveyed cells that a species was detected in)—was used to assess whether there were any trends in occurrence over time for three cetacean species. From this analysis, a significant trend to increasing occurrence of harbour porpoises in summer months in the English Channel was identified. There were also increases in the occurrence of common dolphins in the English Channel in winter months and striped dolphins in the Bay of Biscay in winter months corresponding with a decrease in summer occurrence, across the study period. However, while consistent, these trends were not significant.