Bank erosion is an important source of sediment and phosphorus to inland fluvial systems and is generally responsible for more than half of the total watershed sediment export. Numerous studies have quantified bank erosion and the spatio-temporal variation of sediment flux in different watersheds. However, there is sparse research to date on the linkages between bank erosion/accretion and sediment export under different land uses, especially in rapidly evolving peri-urban watersheds. This research, therefore, integrated remote sensing techniques and repeated field survey of erosion pin plots to quantify bank erosion and sediment flux in the 80 km2 Nkisi River watershed (NRW), southeast Nigeria, over a three-year period. The impact of land use change on streambank erosion was evaluated by utilising remotely sensed Landsat datasets of 2003, 2010, 2016 and 2019. Geotechnical tests were used to characterise the lithologic properties of the banks, while the Bank Stability and Toe Erosion Model (BSTEM) was used to determine the stability of the banks under various hydrological conditions and mechanical properties of the riparian vegetation. Mean bank recession rates increased from 10.7 cm during the 2017–2018 monitoring period to 17.5 cm for the 2019–2020 monitoring period. The percentage of total watershed export ascribed to bank erosion in the three stream reaches varied from 6.6 to 44.9%. The high rates of bank erosion and accretion within the NRW were attributed to rapid changes in land use, which evolved from grassland and woodland to cropland, built-up and bare land. The BSTEM accurately predicted the high erosion rates of the streambanks and showed that riparian vegetation has a mechanical effect on bank stability. However, the mechanical effect diminishes as the depth to water table rises during high streamflow events.