The Arunca River basin in Central Portugal has a historical record of hazardous events related to floods, causing widespread disturbance. This article describes the application of two approaches based on well-known methods for the estimation of flood-prone areas: (i) historical-hydrogeomorphological reconstitution, applied to the entire Arunca River basin, and (ii) hydrological-hydraulic modelling, applied to four sections selected from different (upper, middle and lower) sectors of the basin and including urban and rural areas along the Arunca River. The mapping of the flood-prone areas obtained by these two methods was compared in order to identify the main differences and similarities. Human interventions (river channel and floodplain morphological changes) were found to be the main factor explaining the differences and similarities between the results obtained by both methods. The application of hydrological-hydraulic modelling proved important in reinforcing the results of the historical-hydrogeomorphological method; it also helped in complementing the results produced by the latter method in urban areas and in areas with insufficient historical records. The application of the historical-hydrogeomorphological method, in turn, allowed for the size of the flood-prone areas to be determined where the primary data (e.g. geometry, roughness and flow) was not accurate enough for hydrological-hydraulic modelling. The methodological approach adopted demonstrates the strong complementary relationship between the different existing methods for estimating flood-prone areas, and may be reproduced for other drainage basins.