Objective: Youth drinking is highly heterogenous, and subpopulations representing different alcohol use patterns may have responded differently to the COVID-19 pandemic. This study examined changing patterns of alcohol use in subpopulations of the youth population over the first two years of the pandemic. Method: We used linked survey data from 5367 Canadian secondary school students who participated in three consecutive waves of the COMPASS study between 2018/19 and 2020/21. Latent transition analysis (LTA) was used to identify patterns of alcohol use based on the frequency of drinking and frequency of binge drinking and to estimate the probability of transitioning between identified patterns. Results: LTA identified five patterns of alcohol use each representing a unique subpopulation: abstainer, occasional drinker-no binging, occasional binge drinker, monthly binge drinker, weekly binge drinker. Probability of being engaged in binge drinking for a subpopulation of occasional drinkers pre-pandemic was 61%, which reduced to 43% during the early-pandemic period. A lower proportion of occasional binge drinkers reported moving to monthly or weekly binge drinking. Female occasional drinkers were more likely to move to binge drinking patterns during the pandemic than males. Conclusions: Less frequent drinking and younger students were more likely to reduce their drinking and binge drinking than more established drinkers during the COVID-19 pandemic. Understanding of heterogenous patterns of alcohol drinking and different responses to public health crises may inform future preventive programs tailored to target subpopulations more effectively.