Cardigan Bay on the western coast of the UK is considered a pristine location with much of its coastal and marine habitats protected under various national and EC Directives. Despite this, populations of the flatfish dab (Limanda limanda) captured from Cardigan Bay display elevated levels of liver tumours relative to the background prevalence of the disease. This study describes the findings of a research cruise that took place during November 2003 to assess the prevalence of tumours in dab from selected sites in and around Cardigan Bay. In addition, potential causative mechanisms were investigated via measurement of a range of end points (including composition and abundance of benthic and phytoplankton communities, sediment toxicity and cellular biomarkers of genotoxicity) from sediment, water and biota samples. Fish captured from South Cardigan Bay displayed a relatively higher prevalence of liver tumours compared to those captured from Red Wharf Bay. Hepatocellular adenoma (8% and 2%, respectively) and hepatocellular foci of cell alteration (18% and 6%, respectively) were most prevalent in South Cardigan Bay. Analysis of the sediment failed to distinguish any differences in toxicity between the two sampling sites. However, DNA strand breaks in red blood cells of dab were significantly higher (p < 0.05) in fish collected from Red Warf Bay compared with those sampled at Cardigan Bay. The alignment of biological effects measures via such integrated cruise programs are discussed. This work was partly funded under the auspices of the 2003 Prince Madog Prize.