The biological effects of contaminants in British estuaries and coastal waters have been studied for over 100 years. Until the 1970s, the major pollution impact on estuarine organisms was probably caused by poorly treated sewage which led to severe oxygen deficits and consequent asphyxiation of many water-breathers. However, since the introduction of improved sewage treatment in the last 30 years, a number of continuing impacts have come to light which represent true toxic effects of micro-contaminants. Sublethal changes observed in various bioassays and biomarkers are widespread in both fish and invertebrates, and in the most urbanised and industrialised estuaries, these effects are probably having impacts at the population and community levels. For example, there is good evidence to show that tributyltin from some antifouling paints has not only affected the sexuality and reproductive success of individual estuarine and coastal molluscs, but has also damaged some benthic communities of which molluscs are but a part. Although there are data to show that some contaminant concentrations are now declining, we do not yet have enough data in most cases to decide whether organisms have also begun to recover. This paper reviews the entire field of contaminant effects in UK estuarine and marine waters, focusing especially on the years 1985–2000, and makes some recommendations for future research and monitoring programmes.