Knowledge of using freshwater as a method to remove sea lice from farmed Atlantic salmon (Salmo salar) is limited. A field study was conducted on a specially designed well boat for delousing serving salmon farms to investigate the fate of sea lice on the salmon during freshwater treatment. The parasitic sea lice (Lepeophtheirus salmonis and Caligus elongatus) were registered at five different freshwater treatments at three aquaculture sites. Crowded salmon were pumped onboard to the starboard well and port well, with each well having a capacity of 1600 m3. The range of mean weight for the treated salmon was between 2.87 and 4.65 kg. The first sampling was made during crowding of the salmon from the net pens, followed by three samplings in each freshwater well during the treatment, and one sampling during the unloading of salmon back to the cages. Using freshwater as a delousing method generally had a high efficiency for L. salmonis and C. elongatus. There was a rapid reduction for all stages of L. salmonis and of C. elongatus in the initial phase of the freshwater treatment. The mean reduction for the earliest developmental stages of L. salmonis (sessile and preadult) was 70% and 63%. In contrast, females with egg strings and C. elongatus were almost completely removed within the first sampling (88% and 94%). For the adult stages (male and female without egg strings), there was a slower reduction (49% and 44%), respectively, at the first sampling. It is unclear how strongly the mechanical effect caused by crowding in the initial phase of the treatment affected attached sea lice. The rapid initial decrease in lice numbers might be a combination of freshwater and mechanical effects. There was further a high final reduction during unloading for sessile and preadult (89% and 93%), and for the adult males and females without egg strings and females with egg strings (82%, 88%, and 89%). Some variation was found between stages of L. salmonis as well as between the five treatments. The earlier life stages start with variable numbers before treatment (1.3–6.1 lice fish−1), ending with relatively similar numbers post-treatment. For the older stages, there were variations in lice numbers before freshwater treatment (0.7–2.1 lice fish−1) and after treatments (0.0–0.8 lice fish−1).