The Atlantic salmon aquaculture industry in Norway is frequently confronted by the biological risks associated with the transport, handling, and treatment of live fish in well‐boats. The aim of this study was to collect experience‐based knowledge from the aquaculture industry about well‐boat operations, to make recommendations to lower the biological risk in well‐boat operations. Well‐boat crew, salmon farmers, fish health personnel, and workers in other relevant professions in the industry participated in semi‐structured individual interviews, followed by group interviews and a survey. This study clearly revealed that even though operational/technical factors are critical for lowering the biological risk in well‐boat operations, their successful implementation hinges on three fundamental human factors: (1) experienced personnel in key positions having correct focus, (2) communication, and (3) planning/risk assessment. Those factors deserve greater attention, as the present study highlights that they are not always sufficiently taken into account. An array of recommendations to lower the biological risk for Atlantic salmon in well‐boat operations is identified and summarized based on the findings from the study and literature.