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ABSTRACT Background The COVID-19 pandemic, coupled with concurrent social instabilities, has raised concerns about the long-term impact on the population mental health. While existing studies have primarily focused on the acute phase, less is known about how anxiety and depression symptoms have evolved throughout prolonged societal disruption. This study aimed to identify distinct anxiety and depression symptom trajectories and to determine the individual, relational, and societal protective and risk factors that influence anxiety and depression scores among Belgian adults from 2020 to 2024. Methods We used longitudinal data from five waves of the COVID-19 Health Surveys and the BELHEALTH study (n = 10,063) among Belgian adults, collected between April 2020 and June 2024. Anxiety and depression were assessed using the Generalized Anxiety Disorder-7 and the Patient Health Questionnaire-9, respectively. Covariates were selected based on the social-ecological framework and included both time-invariant and time-dependent variables. Latent class linear mixed models identified subgroups with distinct trajectories. Multilevel linear mixed effects models examined associations between symptom severity and predictors across individual, relationship, and societal levels. The final model, selected based on the lowest AIC (Akaike Information Criterion), included the full set of covariates. Results Four depression and five anxiety trajectories were identified. While most participants maintained stable mild symptoms, 11.3% experienced increasing depression and 8.4% showed increasing anxiety over time. Financial difficulty, female gender, and younger age were overrepresented in moderate and severe symptom trajectories. Protective factors such as social support, satisfying social contact, and life satisfaction were associated with lower symptom severity. Over time, life satisfaction demonstrated an increasing protective effect, while the influence of social contact on reducing symptoms weakened progressively. Risk factors included financial and job-loss worry, loneliness, psychotropic medication use, and high mental health stigma. Conclusions Our results demonstrate persistent heterogeneity in mental health responses, with a substantial share of the population experiencing worsening symptoms years after the pandemic began. Public mental health strategies must therefore go beyond short-term crisis response, address long-term risks such as financial insecurity, social isolation, and stigma, while fostering individual and collective resilience.