We conducted a 12-month follow-up of a population sample of adults from districts (Mannar, Killinochi, Mullaitivu and Jaffna) exposed to high levels of mass conflict in Sri Lanka, the aim of the present analysis being to identify trajectories of depression and anxiety symptoms and their associations with exposure to psychological trauma and ongoing living adversities. The cohort of 1275 adults (response 86%) followed-up in 2015 was a structured subsample drawn from the baseline nationally representative survey conducted in 2014 across 25 districts in Sri Lanka. Interviews were conducted using electronic tablets by field workers applying contextually adapted indices of trauma exposure, ongoing adversities and symptoms of depression and anxiety. Latent transition analysis revealed a three-class longitudinal model from which four composite trajectories were derived, comprising a persistent symptom trajectory (n = 555, 43.5%), an incident or new onset trajectory (n = 170, 13.3%), a recovery trajectory (n = 299, 23.5%) and a persistently low-symptom trajectory (n = 251, 19.7%). Factors associated with both the persistent symptom and incident trajectories were female gender, past trauma exposure and lack of access to health services. Loss of a job was uniquely associated with the persisting trajectory at follow-up. The recovery trajectory comprised a higher proportion of men, older persons and those without risk factors. Our findings assist in translating epidemiologic data into public policy and practice by indicating the importance of stable employment and the provision of healthcare as key factors that may act to reduce anxiety and depressive symptoms in the post-conflict phase. The findings also confirm that women are at high risk of mental distress. Brief screening for trauma exposure in populations with high levels of exposure to mass conflict may assist in defining those at risk of ongoing symptoms of anxiety and depression.