While ample evidence from high-income country settings indicates the prevalence and risk factors for multiple mental ill-health symptoms in student populations, evidence from low- and middle-income higher education settings remains limited. We determined the frequency, associations, and structural pathways between mental health outcomes and possible risk factors among a sample of 1292 predominantly Black African and female students ages 18–30 years, enrolled at nine purposefully selected public universities and Technical Vocational Education and Training (TVET) campuses. We measured and created a mental ill-health latent outcome consisting of depressive symptoms, post-traumatic stress disorder (PTSD), and suicidal thoughts. We also measured traumatic exposures including childhood trauma, recent intimate partner violence (IPV), non-partner rape, and other life traumatic events. We used structural equation modelling to analyse data. We found that 50% of the surveyed students binge drank, 43% reported depressive symptoms, 9% reported PTSD symptoms, and 21% had suicidal thoughts. Students’ experiences of childhood trauma, food insecurity, other traumatic events, non-partner rape, and IPV impacted the mental ill-health latent. IPV experiences mediated the relationships between experiences of childhood trauma or other trauma and the mental ill-health latent, and the relationship between binge drinking and other life traumatic events. Non-partner rape mediated the relationship between food insecurity and the mental ill-health latent. Binge drinking directly impacted non-partner rape experience. The findings substantiate the need for campus-based mental health promotion, psychosocial services and treatments, and implementation of combined interventions that address the intersections of violence against women and mental health among students in South Africa.