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Background The COVID-19 pandemic has led to large proportions of the labour market moving to remote work, while others have become unemployed. Those still at their physical workplace likely face increased risk of infection, compared to other workers. The objective of this paper is to understand the relationship between working arrangements, infection control programs (ICP), and symptoms of anxiety and depression among Canadian workers, not specifically working in healthcare. Methods A convenience-based internet survey of Canadian non-healthcare workers was facilitated through various labour organizations between April 26 and June 6, 2020. A total of 5180 respondents started the survey, of which 3779 were assessed as employed in a full-time or part-time capacity on 2 March 2020 (prior to large-scale COVID-19 pandemic responses in Canada). Of this sample, 3305 (87.5%) had complete information on main exposures and outcomes. Anxiety symptoms were measured using the Generalised Anxiety Disorder screener (GAD-2), and depressive symptoms using the Patient Health Questionnaire screener (PHQ-2). For workers at their physical workplace (site-based workers) we asked questions about the adequacy and implementation of 11 different types of ICP, and the adequacy and supply of eight different types of personal protective equipment (PPE). Respondents were classified as either: working remotely; site-based workers with 100% of their ICP/PPE needs met; site-based workers with 50–99% of ICP/PPE needs met; site-based workers with 1–49% of ICP/PPE needs met; site-based workers with none of ICP/PPE needs met; or no longer employed. Regression analyses examined the association between working arrangements and ICP/PPE adequacy and having GAD-2 and PHQ-2 scores of three and higher (a common screening point in both scales). Models were adjusted for a range of demographic, occupation, workplace, and COVID-19-specific factors. Results A total of 42.3% (95% CI: 40.6–44.0%) of the sample had GAD-2 scores of 3 and higher, and 34.6% (95% CI: 32.–36.2%) had PHQ-2 scores of 3 and higher. In initial analyses, symptoms of anxiety and depression were lowest among those working remotely (35.4 and 27.5%), compared to site-based workers (43.5 and 34.7%) and those who had lost their jobs (44.1 and 35.9%). When adequacy of ICP and PPE was taken into account, the lowest prevalence of anxiety and depressive symptoms was observed among site-based workers with all of their ICP needs being met (29.8% prevalence for GAD-2 scores of 3 and higher, and 23.0% prevalence for PHQ-2 scores of 3 and higher), while the highest prevalence was observed among site-based workers with none of their ICP needs being met (52.3% for GAD-2 scores of 3 and higher, and 45.8% for PHQ-2 scores of 3 and higher). Conclusion Our results suggest that the adequate design and implementation of employer-based ICP have implications for the mental health of site-based workers. As economies re-open the ongoing assessment of ICP and associated mental health outcomes among the workforce is warranted. [ABSTRACT FROM AUTHOR]