Infestations of post-smolt sea trout (Salmo trutta L.) by the salmon louse (Lepeophtheirus salmonis Krøyer) were characterized in 42 estuaries over a 5 year period in Ireland. Spatial variation in infestation was more significant than temporal trends and existed at 3 levels; between regions (regions > 100 km of coastline), between bays within regions (bays < 50 km in length) and between estuaries within bays (distance between estuaries < 10 km). The observed spatial structure in infestations inferred that production of the infective larvae varied between regions and bays and that there was limited movement of fish and infective larvae between regions and bays. In addition the different levels of infestation recorded between estuaries in the same bay indicated short spatial scale variability in parasite transmission. Significantly higher infestations occurred in bays that contained lice-infested farmed salmon. Lice-infested wild spring salmon, which were present in estuaries of some systems, did not have a significant positive impact on infestations.