This research focused on the specific diversity of diatoms carried in ballast sediments of ships reaching Canadian ports on the Pacific, Atlantic and the Great Lakes during 2007 and 2009. The inventory of 180 taxa included Thalassiosira, Chaetoceros spores, Cyclotella, Actinocyclus, Aulacoseira, Melosira and Pseudo-nitzschia as the most species-rich genera found in 142 samples of the matter settled at the bottom of ship tanks. We also tested and showed evidence that diatom species composition identified in any given tank was the product of: (i) species intrinsic survival strategies, (ii) the most recent ballast water exchange (BWE), and (iii) the cumulative end result of past ballast operations. Multivariate analysis reduced our data set to three assemblages. Propagule pressure of these potentially colonizing assemblages may be enhanced due to repeated introduction attempts by ships belonging to different ballast management categories (transoceanic, intra-coastal with our without BWE) but that actually carried the same assemblage type. A non-linear relationship between colonization and propagule pressure confirms that the early stages of invasion (ballast uptake, survival in the tank) structure the later stages. Coastal floras in tanks that underwent offshore BWE (particularly persisting freshwater species) corroborate concern with the low efficiency of this management option.