Core Ideas Yield of canola and mustard was associated with total dry matter production and seeds m−2. The yield penalty for triazine‐tolerant cultivars was lower in the season with dry spring. Seed yield of canola and mustard was highly responsive to the application of N at the rosette stage. Yield with 100 kg ha−1 N at rosette was equivalent to 85 and 94% of the maximum in canola and mustard. Increasing the sink capacity by improving the pre‐flowering crop biomass has an important influence on seed yield of canola and mustard. Altering the amount and the timing of N according to phenological development can be an effective way of managing variation in seasonal rainfall, which could improve seed yield. The aim of this study was to investigate the effect of post‐sowing N applications at different phenological growth stages on the seed yield of different canola (Brassica napus L.) and mustard [Brassica juncea (L.) Czern. & Coss.] cultivars. Field experiments were conducted in South Australia with four canola and two mustard cultivars. All cultivars were grown under different N treatments, which included two rates (100 and 200 kg ha−1) and four (2011) or five (2012) times of application at specific growth stages (rosette, green bud, flowering, pod initiation, and pod development). Mustard and canola performed similarly in an average rainfall season but canola out‐yielded mustard in the season with below‐average rainfall. Seed yield of canola and mustard was found to be closely associated with total dry matter production and seeds m−2. The yield penalty for triazine‐tolerant (TT) cultivars was lower in the season with a dry spring than in the season with average rainfall. Application of 100 kg N ha−1 at the rosette stage produced yield equivalent to 85% of the maximum in canola and 94% of the maximum in mustard, which was achieved with the application of 200 kg N ha−1 in five equal splits. These results suggest that increasing the sink capacity by improving the pre‐flowering crop biomass has an important influence on seed yield of canola and mustard.