The available data for two important Irish estuaries, Cork and Wexford harbours, were analysed to identify 'hot spots': locations where water quality variables are likely to differ from background levels. The approach taken reflects the limitations imposed by restricted spatial and temporal replication in the available datasets. Information for many estuaries may exist in such fragmented datasets. Averages drawn from small sample sizes are susceptible to extreme values. To lessen this problem, a novel approach was used: identifying locations where high measurements of a variable were relatively more frequent. The locations of relatively high chlorophyll measurements in Cork and Wexford harbours indicated estuarine origins for the majority of algal blooms. Nutrient cycling in Wexford Harbour appeared to be coupled with phytoplankton growth. The estuary acted as a source for dissolved inorganic nutrients during periods with low chlorophyll levels and as a sink during plankton blooms. High chlorophyll levels in Cork Harbour were generally associated with sub-surface samples in stratified water. Sources of ammonia and phosphate in Cork harbour appeared to result from direct anthropogenic input. Residual variation in biological oxygen demand reflected point pollution sources in both Cork and Wexford Harbours. Algal blooms were common in both estuaries, with 20% of chlorophyll a measurements exceeding 20 mug l(-1) in each system. However, despite the presence of blooms and influences of point sources, there is currently little evidence for environmental impacts such as extensive deoxygenation. This conclusion is tentative, given the fragmented nature of the datasets. The locations of hot spots can be used to inform future research on potential impacts and estuarine function.