Effectiveness of sea lice bath treatment is often assessed by comparing pre‐ and post‐treatment counts. However, in practice, the post‐treatment counting window varies from the day of treatment to several days after treatment. In this study, we assess the effect of post‐treatment lag time on sea lice abundance estimates after chemical bath treatment using data from the sea lice data management program (Fish‐iTrends) between 2010 and 2014. Data on two life stages, (i) adult female (AF) and (ii) pre‐adult and adult male (PAAM), were aggregated at the cage level and log‐transformed. Average sea lice counts by post‐treatment lag time were computed for AF and PAAM and compared relative to treatment day, using linear mixed models. There were 720 observations (treatment events) that uniquely matched pre‐ and post‐treatment counts from 53 farms. Lag time had a significant effect on the estimated sea lice abundance, which was influenced by season and pre‐treatment sea lice levels. During summer, sea lice were at a minimum when counted 1 day post‐treatment irrespective of pre‐treatment sea lice levels, whereas in the spring and autumn, low levels were observed for PAAM over a longer interval of time, provided the pre‐treatment sea lice levels were >5–10.