Fish farming is the fastest growing food production sector worldwide and now accounts for most human fish consumption. Expansion of finfish aquaculture to exposed offshore marine environments is appealing where additional sheltered areas are unavailable. While more energetic environments may reduce waste accumulation and parasite exposure, effects on fish health and wellbeing are largely speculative. The multiple stressors faced by fish on offshore farms may interact synergistically and increase their cumulative impact. We used 20 months of health and welfare data from eight Atlantic salmon (Salmo salar) sea pen farms in Scotland along a wave exposure gradient to assess the effects of, and interactions between, environmental variables and management treatments on fish mortality and parasite loads. While farms showed high variability in mortality rate and sea lice infections, multi-level Bayesian modelling indicated that wave exposure primarily modulated effects of other variables. Higher exposure farms showed steeper increases in mortality with time and with extreme temperatures. Similarly, sea lice infections tended to increase with time, with higher exposure farms seeing steeper increases at higher Amoebic Gill Disease (AGD) scores and at high temperatures. The effect of AGD was greater at slow water speeds. Treatments against parasites were more frequent at low exposure farms, leading to uncertainty in their impact on welfare across farms. The support for interactive effects of wave exposure with other variables rather than strong direct effects suggests an accumulation of chronic and acute stressors. Expansion of aquaculture to more energetic offshore environments may have negative impacts on fish health in some circumstances, requiring adaptation of practices. In particular, the stronger increase in mortality over time may have implications for cycle length in different environments, and the more dramatic impacts of the warmest temperatures at high exposure farms call for consideration of the change in water temperature both inshore and offshore.