Since 2007 about 200 to 300 fish per year – generally roach (Rutilus rutilus) also a few bleak (Alburnus alburnus) and eels (Anguilla anguilla) – have been collected from a number of English river sites and stored at − 80 °C to build up a Fish Tissue Archive as a resource for the monitoring of pollutants. Some of the fish from the Fish Tissue Archive from the years 2007–2011 were analyzed for substances in current and proposed European legislation regarding environmental quality standards (EQS) in biota. It was found that mercury exceeded the EU EQS of 20 μg/kg in 79% of samples with an average and median of 31 and 29 μg/kg. The legacy fungicide hexachlorobenzene (HCB) was below the EQS of 10 μg/kg in all fish analyzed, with a maximum of 6 μg/kg in some eels. The legacy solvent hexachlorobutadiene (HCBD) was below the EQS of 55 μg/kg, being < 0.2 μg/kg in all samples where it was measured. The sums of six polybrominated diphenyl ethers (PBDEs) were several orders of magnitude higher than the new proposed 0.0085 μg/kg biota EQS. This study showed that the regular collection and analysis of whole body homogenate samples of relatively small native pelagic fish is suitable for the monitoring of contaminants capable of bioaccumulation. With regard to current or proposed EQS for EU countries, mercury and potentially PBDE in fish are of some concern in these English rivers.