Electronic structure methods are combined into a multiscale framework to investigate the electronic transport properties of recently synthesized pristine and nitrogen-doped graphene nanowiggles and their heterojunctions deposited on a substrate. Real-space Kubo-Greenwood transport calculations reveal that charge carrier mobilities reach values up to 1000 cm² V1 s1 as long as the amount of substrate impurities is sufficiently low. Owing to their type-II band alignment, atomically precise heterostructures between pristine and N-doped graphene nanowiggles are predicted to be excellent candidates for charge carrier separation devices with potential in photoelectric and photocatalytic water splitting applications.