Facultative anadromous salmonids may alter migratory behaviour to mitigate against detrimental infections of aquaculture-derived salmon lice (Lepeophtherius salmonis), however this likely incurs negative growth and fitness consequences. This flexibility in migratory behaviour also creates analytical challenges in estimating lice infestation levels and the direct/indirect consequences of exposure. We utilised simulated individual migration trajectories of facultatively anadromous brown trout (Salmo trutta) (N=8049), generated from spatial-temporal fjord-use models fitted to empirical tracking data (N=517). These trajectories were superimposed with open-access spatial-temporal modelled lice densities. Individual accumulated lice exposure and infestation was simulated over a six-month period for smolts and annually for veteran migrant life-stages. The degree of direct and indirect mortality was estimated according to year (2013–2015), population (N=5) and life-stage of brown trout, within a semi-enclosed fjord system (Sognefjorden, Norway). A gradient of lice was spatially distributed throughout the fjord. Highest densities were modelled in the outer-fjord at a closer vicinity to aquaculture facilities. As most brown trout remained in the inner-fjord, an area protected from aquaculture, accumulated levels of lice exposure and infestation were low, resulting in limited direct mortality (smolts: 0.07 %, veteran migrants: 0.04 %). Accumulated lice infestation was higher for individuals that underwent long-distance migrations, residing for longer in the outer-fjord, with limited differences observed between years. Indirect mortality attributable to lice was greater for long-distance migrants (smolts: 25.3 %, veteran migrants: 14.8 %), versus those remaining within the inner-fjord (smolts: 14.7 %, veteran migrants: 1.7 %). This resulted in an unequal lice-induced mortality loss among populations (range: 3.3– 34.3 %).

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Norwegian Veterinary Institute (NVI) model of SLenv was requested directly from the authors.