We developed generalised additive models (GAMs) to estimate standardised time-series of population abundance indices for assessment purposes and to infer ecological and behavioural information on northern Benguela hakes, Merluccius capensis and M. paradoxus, using haul-by-haul commercial trawl catch-rate data as proxies for hake densities. The modelling indicated that individual ship identifiers should be used rather than general vessel characteristics, such as vessel size. The final models explained 79% and 68% of the variability in the commercial catch rates of M. capensis and M. paradoxus, respectively. The spatial density patterns were consistent and confirmed existing knowledge about these species in the northern Benguela system. Furthermore, seasonal migration patterns were described for the first time and were found to correspond to the known spawning areas and seasons for M. capensis and M. paradoxus. Spatial density patterns were validated using the geostatistical modelling results of fisheries-independent trawl survey data. Improved understanding of the relationships between fleet dynamics and fish movement can be achieved by taking into consideration the present catch-rate model and spatial and seasonal distribution maps. We conclude that the yearly standardised CPUE time-series are problematic as proxies for total stock abundance because of spatial coverage issues. Consequently, such CPUE data should not be used for stock-size assessments and fisheries advice concerning northern Benguela hakes until this is solved. We generally recommend the exclusion of standardised CPUE time-series from stock assessments when important and changing parts of the stock distribution cannot be targeted by the fishery, such as due to closed areas or seasons.