Both the salmon louse Lepeophtheirus salmonis and its close relative Caligus elongatus are ectoparasitic on Salmonidae in salt water in the northern hemisphere. In this study we monitored population dynamics of these parasites on anadromous brown trout, i.e. sea trout, on the Norwegian Skagerrak coast in the winters of 1998–1999 and 1999–2000. The low salinity was expected to reduce sea lice populations as lice do not tolerate sojourns of more than a few weeks, at most, in freshwater. Results confirmed the presence of both parasite species on estuarine sea trout in winter, and showed that the lice populations go through a bottleneck in this period. Prevalences of infection of both parasite species were very different in the two sampling periods, but fell below 10% in March in both winters. Median infection intensity was 1–2 fish−1. Salinity was statistically related to the presence of C. elongatus both winters, and to L. salmonis in 1999–2000. Temperature appeared to be less important for the abundance of lice.