Background: Population-based surveys document disparities in substance use among sexual minorities compared to heterosexuals, but few studies examine changes over time. This study compared changes in harmful drinking (including alcohol use disorders and high-intensity drinking), tobacco use, marijuana use, and simultaneous marijuana and alcohol co-use between heterosexual and sexual minority adults over a 15-year period. Methods: Gender-stratified logistic regression analyses using 4 waves of cross-sectional data from the National Alcohol Survey (2000, 2005, 2010, and 2015) were conducted to test overall trends over time and differences by sexual identity, as well as the interaction between survey year and sexual identity. Results: Among women, significant effects for sexual identity were present in all models, reflecting greater odds of use among sexual minorities across waves. Among men, significant effects for sexual identity were found for high-intensity drinking (reflecting less use among sexual minorities) as well as marijuana use and marijuana and alcohol co-use (reflecting more use among sexual minorities). For women and men, tobacco use generally decreased and both marijuana use and simultaneous marijuana and alcohol co-use increased during the study period. Although trends were largely driven by heterosexual respondents, only one instance of an interactive effect was found; reports of harmful drinking were generally stable over time among heterosexual women, but higher and more variable over time among sexual minority women. Conclusions: Findings highlight that differences in patterns of substance use by sexual identity persist and underscore the need for screening, prevention, and intervention, particularly for sexual minority women.