The major by-catch species retained during twice yearly dredge surveys of great scallop, Pecten maximus, and queen scallop, Aequipecten opercularis, (both Mollusca: Pectinidae) populations on 13 fishing grounds in the northern Irish Sea, over a period of five years, were identified and enumerated. Additionally, the damage sustained by the by-catch was assessed and related to a range of physical parameters recorded during the survey. A number of species captured in the spring-toothed dredges exhibited differences in abundance and damage sustained between years, and also between the start and end of the closed season for great scallop fishing (1 June–31 October). The by-catch assemblage varied geographically, dependent upon the underlying community structure, as well as putative factors including gear efficiency and substratum type. Two clear assemblage types were identified by multivariate analysis, one to the south-west of the Isle of Man, the other covering fishing grounds to the north, east and south of the island. There is a hierarchy of species sensitivity to damage in great and queen scallop dredges, probably related to morphological and behavioural characteristics. This selective mortality of a fraction of the community may have long-term implications at the ecosystem level. The degree of damage sustained by many species is related to both the volume of stones retained in the dredge, and the total volume of the catch (dredge fullness). If these were reduced, the overall magnitude of incidental by-catch mortality would be lower.