Amoebic gill disease (AGD) is the most serious health problem in Atlantic salmon cultured in Tasmania. Our field investigation examined prevalence of AGD during 2 years, every year for up to 7 months after transfer to sea water. The relationship between environmental factors and AGD prevalence was determined. Additionally, effects of adding levamisole to freshwater baths were investigated in a field trial. AGD was recorded on all farms, except for farm A, which did not move salmon from a brackish site to a full-salinity site during the study. The prevalence showed a bimodal distribution with the first larger peak in summer (usually in January) and the second smaller peak in autumn (between March and May). During both years the prevalence of AGD was significantly greater in January than any other month. Sampling month and the interaction between farm and month had a statistically significant effect on AGD prevalence. AGD was recorded at a minimum temperature of 10.6 °C and minimum salinity of 7.2 ppt. There was a positive relationship between the time since the freshwater bath and the prevalence of AGD for the first 30 days after the bath, with a dramatic increase in the AGD prevalence about 3 weeks after the bath. After 30 days, there was no statistically significant relationship between AGD prevalence and days since the last bath, except for the second bath. The addition of levamisole to the freshwater bath did not significantly increase the time between treatments. The relationship between diagnosis on the basis of gross signs and histological diagnosis was significant, however, the gross diagnosis was unreliable within the lower range, with 31.8% false negatives and 15.9% false positives and kappa value of 0.2742.