Sea trout are parasitized by two species of caligid copepod sea lice, Lepeophtheirus salmonis and Caligus elongatus. Generally, levels of lice infestation are low and few adverse effects on the host have been reported. However, with the advent of marine salmon farming since the 1980s, there have been many published accounts of L. salmonis sea lice epizootics on salmonids in aquaculture areas. Few large-scale studies are available on levels of sea lice infestation of sea trout in areas without salmon farms or before their development. Understanding natural background lice levels on sea trout is important to interpret lice levels on trout in aquaculture areas. The Celtic Sea Trout Project, an INTERREG IVA Ireland Wales EU funded project, examined the status, distribution, genetics, and ecology of sea trout around the Irish Sea and provided an opportunity to assess levels of lice on sea trout spatially and temporally in an area without marine salmon farming. The prevalence of L. salmonis remained constant over the 3 years (63–69%), whereas the prevalence of C. elongatus was lower (20–40%). The mean abundance of L. salmonis ranged from 3.6 to 3.8 and that of C. elongatus ranged from 0.6 to 4.3 (n = 850). There was a significant variation in L. salmonis abundance between marine areas. However, the relative stability in the prevalence and mean intensity of both lice species observed and the low mean abundances and very small proportion of juvenile life stages of L. salmonis reported here are similar to those reported from other studies in areas without salmon farming and likely represent natural background salmon lice levels on sea trout. This 3-year study, conducted over a wide geographic area, represents one of the largest studies of sea lice infestation patterns on sea trout in an area distant from finfish aquaculture influences.