Substance use is common in the general population and has been associated with major public health problems including a wide range of psychiatric disorders. Of these disorders, anxiety and depression are common and are associated with significant burden. The coexistence of substance use with other psychiatric disorders has been reported by various international authors. This co-occurrence is referred to as psychiatric co-morbidity. There are however, few studies that addressed the issue of anxiety and depression among those with substance use especially in this environment. Hence, the aim of this study is to determine the prevalence of anxiety and depression among individuals with substance use. The study was a community based study conducted in Lagos Island LGA. A total of 418 substance users were recruited using the snowballing technique after an initial identification of an ex-drug user. All the subjects were interviewed using a socio-demographic questionnaire, substance-use questionnaire which contained details of drug use. Psychiatric diagnosis was made using the PHQ-9 which is a strong tool for diagnosing depression and the MINI which was designed as a brief structured interview for the major Axis I psychiatric disorders in DSM-IV and ICD-10. Data analysis was carried out with SPSS version 15. Statistical analyses were carried out as appropriate. A high proportion of the subjects were using alcohol (97.6%), tobacco (94.7%) and cannabis (89.6%). The prevalence rate of anxiety disorder was 37.8% while, depression had a prevalence rate of 42.1% among the subjects. Socio-demographic factors that were significantly associated with anxiety were young age ( p=0.049), sex (p=0.00), marital status (p=0.001), unemployment (p=0.030) and age of onset of substance use (p=0.042). Clinical factors that were significantly associated with anxiety disorders were multiple substance use (p=0.000 ), longer duration of substance use ((heroin,p=0.000), cannabis (p=0.000), cocaine (p=0.001), alcohol (p=0.001), tobacco (p=0.003)) and frequent substance use ((heroin, p=0.000), cannabis (p=0.007), cocaine (p=0.0001), alcohol (p=0.003), tobacco (p=0.003)). Socio-demographic factors that were significantly associated with depression were sex (p=0.000), Age (p=0.000), marital status (p=0.04), unemployment (p=0.019), education (p=0.03). The clinical factors that were significantly associated with depression were age of onset of drug use (p=0.015), multiple substance use (p=0.000), longer duration of substance use ((heroin, p=0.000), cannabis (p=0.000), cocaine (p=0.001), alcohol (p=0.001), tobacco (p=0.003), frequent substance use ((heroin, p=0.001), cannabis (p=0.04), cocaine (p=0.001), alcohol (p=0.003), tobacco (p=0.003). The results of this study showed that anxiety and depression are common among individuals with substance use. The study also found that various socio-demographic and clinical variables are significantly associated with anxiety and depression among substance users. These variables should therefore be factored into their management. It is important to know that the cross-sectional nature of the study made it difficult to establish causality; as such a longitudinal study may be more helpful in determining the relationship between psychoactive substance use and psychiatric morbidity.