The results of this study showed considerable heterogeneity in the patterns of substance use across the diagnostic groups studied, which became exceedingly apparent after examining the moderating effects of gender. Reported rates of alcohol and cannabis tended to be the highest within 30-days of hospitalization, regardless of diagnosis, and more males continued to use these substances over the follow-up compared to females. Furthermore, patients with bipolar disorder were particularly at risk for continued cannabis use throughout the study, and women with depression were more likely to stop using alcohol whereas men with schizophrenia tended to be the most likely to stop their alcohol use. Regardless, both alcohol and cannabis were associated with poorer symptom and functional outcomes. This study reports results showing substance use is associated with poor outcomes, and that the use of alcohol and cannabis varies by gender and diagnosis, suggesting that personalizing substance use interventions to the psychiatric condition and gender of the patient may be most effective in achieving recovery for individuals with co-occurring conditions.