Congenital heart disease (CHD) is a serious anomaly for which the etiology remains elusive. We explored temporal trend associations between industrial developmental toxicant (DT) air emissions and CHD in Alberta. Patients born between 2004–2011 with a diagnosis of CHD and 18 DTs from the National Pollutant Release Inventory (2003–2010) were identified. We applied principal component analysis (PCA) to DT amounts and toxicity risk scores (RS) and defined yearly crude CHD and septal defects rates for urban and rural regions. Correlations between DT groups and CHD rates were examined with Spearman test and Bonferroni correction was conducted for multiple comparisons. PCA identified three DT groups: Group 1 (volatile organic compounds (VOCs) and other gases,) Group 2 (other VOCs), and Group 3 (mainly heavy metals). Province-wide, we found associations between Group 1 DTs and CHD and septal defect rates, when using amounts (r = 0.86, CI 0.39, 0.97 and r = 0.89, CI 0.48, 0.98, respectively) and RS (r = 0.88, CI 0.47, 0.98 and r = 0.85, CI 0.36, 0.97, respectively). Rural Group 2 DTs were positively associated with septal defect rates in both amounts released and RS (r = 0.91, CI 0.55, 0.98 and r = 0.91, CI 0.55, 0.98, respectively). In this exploratory study, we found a temporal decrease in emissions and CHD rates in rural regions and a potential positive association between CHD and septal defect rates and mixtures of organic compounds with or without gases.