This study aimed to determine whether higher intakes of Na, added sugars and saturated fat are prospectively associated with all-cause mortality and CVD incidence and mortality in a diverse population. The nationally representative Canadian Community Health Survey-Nutrition 2004 was linked with the Canadian Vital Statistics – Death Database and the Discharge Abstract Database (2004–2011). Outcomes were all-cause mortality and CVD incidence and mortality. There were 1722 mortality cases within 115 566 person-years of follow-up (median (interquartile range) of 7·48 (7·22–7·70) years). There was no statistically significant association between Na density or energy from saturated fat and all-cause mortality or CVD events for all models investigated. The association of usual percentage of energy from added sugars and all-cause mortality was significant in the base model with participants consuming 11·47 % of energy from added sugars having 1·34 (95 % CI 1·01, 1·77) times higher risk of all-cause mortality compared with those consuming 4·17 % of energy from added sugars. Overall, our results did not find statistically significant associations between the three nutrients and risk of all-cause mortality or CVD events at the population level in Canada. Large-scale linked national nutrition datasets may not have the discrimination to identify prospective impacts of nutrients on health measures.