A conspicuous part of the parasite fauna of marine fish are ectoparasites, which attach mainly to the fins or gills. The abundant copepods have received much interest due to their negative effects on hosts. However, for many localities the copepod fauna of fish is still poorly known, and we know little about their temporal stability as long-term observations are largely absent. Our study provides the first inventory of ectoparasitic copepods on fish from the western Wadden Sea (North Sea) based on field data from 1968 and 2010 and additional unpublished notes. In total, 47 copepod parasite species have been recorded on 52 fish host species to date. For two copepod species parasitizing the European flounder (Platichthys flesus), a quantitative comparison of infection levels between 1968 and 2010 was possible. Whereas Acanthochondria cornuta did not show a change in the relationship between host size and infection levels, Lepeophtheirus pectoralis shifted towards the infection of smaller hosts, with higher infection levels in 2010 compared to 1968. These differences probably reflect the biology of the species and the observed decrease in abundance and size of flounders during the last decades. The skin-infecting L. pectoralis can probably compensate for dwindling host abundance by infecting smaller fish and increasing its abundance per given host size. In contrast, the gill cavity inhabiting A. cornuta probably faces a spatial constraint (fixed number of gill arches), thus limiting its abundance and setting a minimum for the host size necessary for infections.