In aquaculture, effective parasite management often relies on chemical therapy when prevention strategies are ineffective. Fish are often medicated using immersion (bath) treatments. The efficacy of bath treatment relies on maintaining at least the minimum effective dose for the necessary treatment duration. Dose is influenced by the product used, calculation of system volume, application method, flow, mixing, treatment degradation rate and environmental conditions. To maximize efficacy the relationships between system, delivery and effective dose need to be understood or controlled. We tested four application methods using sodium percarbonate (SPC) and two application methods using formalin (FOR, 37% formaldehyde [FA]) in four semi-closed flow-through systems on four Australian freshwater trout farms with different flow and water quality characteristics. Target dose was 64. mg/L SPC and 200. mg/L FOR. Hydrogen peroxide (HP) released from SPC was measured photometrically and FA levels were measured colorimetrically. Each application method achieved consistent doses across repeated applications but not all methods resulted in the dose reaching the target concentration in all parts of the system for the whole treatment duration. Eliminating the influence of system variables by creating static baths provides the most stable treatment environment. Where this is not possible, minimising system variables by modifying flow assists in retaining treatment in the system and improving accuracy of delivered doses. Treatment methods must be validated in a system prior to being routinely applied and mechanisms to optimise dose-duration identified and implemented.