A requirement of the Water Framework Directive (WFD) is that benthic macro-invertebrates must be sampled from coastal and transitional waters at least twice within a river basin cycle (6 years) in order to classify these waterbodies. Numerous samples will be taken from sites in matched habitats throughout the water body. Sampling and analysis is carried out according to established protocols. The Directive requires the monitoring of nominated coastal and transitional waters for benthic macro-invertebrates. This includes the field sampling, processing and analysis of samples. In addition, grab samples have been taken on vessels of opportunity and are considered suitable to fulfill obligations under the WFD. For each grab sample collected this dataset contains: lists and abundance of benthic species >1mm, sediment particle size analysis (PSA), and an estimate of organic matter (LOI). Benthic macro-invertebrates monitoring in transitional and coastal waters under the Water Framework Directive in association with the Environmental Protection Agency