Objective: To identify patterns of adolescent substance use and associated behavioral health characteristics among adolescents. Methods: We conducted a cross-sectional study of 167,504 adolescents aged 13-17 who were screened for substance use, mental health symptoms, and interpersonal violence during well-check visits in a large healthcare system in California from 2021 to 2022. We conducted latent class analysis to identify patterns of substance use from four substance use behaviors (past-year alcohol, cannabis, other substance, and close friends' use). We calculated the prevalence of depressive symptoms, suicidal ideation, bullying, physical abuse by an adult, sexual violence, and intimate partner violence for each substance use class compared to those with no reported substance use behaviors and estimated adjusted prevalence ratios using modified Poisson regression. Results: In total, 29,288 (17 %) adolescents reported >= 1 substance use characteristic. From those, we identified five latent classes with different patterns of substance use: substance use among close friends (37 %), alcohol use (21 %), polysubstance use (20 %), cannabis use and some polysubstance use (18 %), and other substance use (5 %). All classes had higher adjusted prevalence of mental health and interpersonal violence outcomes compared to those with no substance use characteristics, with the greatest differences being among the polysubstance use class. Conclusions: The high prevalence of mental health and interpersonal violence outcomes among adolescents with substance use, even among those who only report close friends' substance use, highlights the need for routine screening during well-check visits. Comprehensive routine social and behavioral health screening among adolescents is vital for early identification and intervention.