Amoebic gill disease (AGD) and sea lice are two of the most significant disease issues facing the Norwegian Atlantic salmon aquaculture industry. Although both diseases respond to various extents, to freshwater treatment, the chemistry, interactions and efficacy of treatment can be variable. These variations can have significant impacts upon the success and failure of treatment and costs to the production cycle. Although it is known that soft freshwater is most effective in bathing of Atlantic salmon with AGD and that most of the freshwaters in Norway fall into the soft category, the low alkalinity and buffering capacity of such water s may impact on the pH and metal toxicity of the water source in use. Similarly dissolved organic carbon can be beneficial in treatment, although sequestration of metal ions can be reversed as the water pH drops due to high densities of fish and accumulations of carbon dioxide. Alternative treatments such as the use of oxidative disinfectants such as hydrogen peroxide used for AGD and sea lice control may have potential although the interactions in seawater with organic loads and dissolved organic carbon are unclear. Similarly the use of oxidative disinfectants in freshwater will depend upon the water chemistry and interactions with treatment chemicals, fish and water organic content. It is recommended that best practice model is required to understand the interactions of water chemistry, fish loading and treatment chemicals in the efficacy of treatments for AGD and sea lice under Norwegian conditions.