As part of the national monitoring programme under the Water Framework Directive (WFD), seine, trawl and fyke net samples were taken of fish from thirteen locations in Tidal Freshwater Transitional Waters (TFTW) around Ireland. The results were highly variable, with some hauls completely empty while others returned high numbers of individuals, usually dominated by a single species. Thirty-four species were recorded, of which Pomatoschistus microps and Platichthys flesus accounted for 63% of all individuals. Seine netting was the most successful in terms of both number of species and abundance, and consequently had the highest diversity metric values. The fish communities of the Lee, the Tolka and the Slaney systems were significantly different from the others. While the Lee had markedly fewer species (S 03) and lower abundance (N08) than the rest, the Tolka had relatively high S ( 13) and the highest total abundance (N04,089). In terms of ecological quality standards (EcoQS), the relative consistency of diversity metrics offers some prospect of setting meaningful quality thresholds. Multimetric indices, incorporating fish guild and functional criteria could be more reliable, but the actual thresholds may have to be linked to the individual systems.