Cannabis (B = 1.65 [95% CI = .83 to 2.47], p < .001) and alcohol (B = 1.04 [95% CI = .36 to 1.72], p = .002) use were both associated with consistently higher BPRS scores. Similarly, cannabis (B = −2.33 [95% CI = −3.67 to −.99], p = .001) and alcohol (B = −1.45 [95% CI = −2.59 to −.32], p = .012) use were also associated with poorer functional outcomes. Although no significant differences were observed between diagnostic groups for these outcomes over the follow-up, moderator model results showed significant interactions between diagnostic groups and gender with regard to the associations between alcohol, but not cannabis use and psychopathology and functional outcomes. Females with schizophrenia-spectrum disorders who used alcohol displayed higher levels of psychopathology compared to other diagnostic groups and their male counterparts, F(2, 2561) = 4.27, p = .014. Males with bipolar and depressive disorders who used alcohol exhibited poor functioning compared to their female counterparts, F(2, 2872) = 5.64, p = .004.