Salmon lice (Lepeophtheirus salmonis) represent one of the most serious pathogens of sea-farmed and wild Atlantic salmon (Salmo salar). During the last decades, intensive fish farming in the fjords have led to higher concentrations of sea lice in these areas. Atlantic salmon utilize these areas when migrating from the rivers to the sea. There is often a brackish water layer in the fjord areas during spring. Sea lice usually avoid low salinity water. Acoustic telemetry techniques were used to record time and swimming depths of Atlantic salmon post-smolts during their out-migration to the sea. Migratory routes were estimated and mapped using GIS technology. Salinity was measured in different parts of the fjord areas and was interpolated to the whole fjord system using GIS technology.

Atlantic salmon post smolts mainly utilize the middle areas of the fjord for their migration to the sea and they swim at different depths depending on the light intensity (means of 0.5m during day and 2.0m during night). A good knowledge of the Atlantic salmon post-smolts migratory routes, swimming depth and the time they stay in the fjord areas will contribute to a better management of the salmon farms in these areas.

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