Warm water treatment has in recent years become widely used for ridding salmonids of sea lice in aquaculture although the consequences of the treatment for fish welfare are not adequately investigated. The objective of this study was to document potential long-term welfare effects of repeated warm water treatments on Atlantic salmon (Salmo salar). Five weeks after a baseline welfare indicator scoring, non-anaesthetised Atlantic salmon (w¯ = 1379 ± 313 g, n = 332) were treated individually in a chamber with seawater at a temperature of 34 °C (warm water treatment) or 9 °C (control treatment) for 30 s. The treatment was repeated after 23–24 days. During the second treatment, a subset of the fish was video recorded for behavioural analysis. Seventeen to eighteen days after the second treatment, welfare indicators were again scored, and organ samples were taken for histopathological examination. The repeated warm water treatments resulted in a significantly increased prevalence and/or severity of scale losses, snout wounds, various eye problems, and active fin injuries as well as a significantly reduced specific growth rate. The fish displayed an immediate, strong behavioural reaction when exposed to warm water, which was probably the main cause of the detected injuries.