The survival of the highly endangered, anadromous fish species North Sea houting (Coregonus oxyrinchus) depends on the correct timing of downstream dispersal during its early ontogenetic stages. To date, however, no studies have investigated the ontogenetic differentiation of swimming performance and behaviour, including the potential of habitat complexity to influence dispersal rates. By testing larval and juvenile North Sea houting in a laboratory, we examined (1) swimming performance measured as maximum swimming performance (Umax) and routine swimming speed (Uroutine) and (2) the potential of habitat complexity (i.e., cover providing shade) to influence dispersal behaviour in an indoor stream channel. The Umax and the Uroutine were 9.4 and 4.6cm s-1, respectively, in the larvae [body length (BL) s-1: 7.3 and 3.5, respectively], and 25.2 and 16.3 cm s-1 in the juveniles (BL s-1: 7.0 and 5.2, respectively). We compared laboratory swimming performance data with water speeds in North Sea houting spawning areas in the Danish River Vidaa. Results showed that the water speeds present in 95% and 85% of the water column caused downstream displacement of larvae and juveniles, respectively. However, areas with slow-flowing water near river banks and river beds could function as nursery habitats. Stream channel experiments showed that cover providing shade caused delayed dispersal in both larvae and juveniles, but the larvae dispersed later and spent less time under cover than the juveniles, a finding that implies ontogenetic effects. Finally, the larvae refused to cross an upstream-positioned cover, a behaviour that was not observed in the juveniles. Therefore, habitat complexity may have the potential to influence dispersal behaviour in both larval and juvenile North Sea houting. Overall, we provided the first evidence of ontogenetic differentiation in the North Sea houting. These findings will be valuable for the development and dissemination of science-based conservation strategies.