Understanding spatial patterns of influenza transmission is important for designing control measures. We investigate spatial patterns of laboratory-confirmed influenza A across Canada from October 1999 to August 2012. A statistical analysis (generalized linear model) of the seasonal epidemics in this time period establishes a clear spatio-temporal pattern, with influenza emerging earlier in western provinces. Early emergence is also correlated with low temperature and low absolute humidity in the autumn. For the richer data from the 2009 pandemic, a mechanistic mathematical analysis, based on a transmission model, shows that both school terms and weather had important effects on pandemic influenza transmission.