Understanding the effects of major hydrogeological controls on hyporheic exchange and bank storage is essential for river water management, groundwater abstraction, restoration and ecosystem sustainability. Analytical models cannot adequately represent complex settings with, for example, transient boundary conditions, varying geometry of surface water-groundwater interface, unsaturated and overland flow, etc. To understand the influence of parameters such as (1) sloping river banks, (2) varying hydraulic conductivity of the riverbed and (3) different river discharge wave scenarios on hyporheic exchange characteristics such as (a) bank storage, (b) return flows and (c) residence time, a 2-D hydrogeological conceptual model and, subsequently, an adequate numerical model were developed. The numerical model was calibrated against observations in the aquifer adjacent to the hydropower-regulated Lule River, northern Sweden, which has predominantly diurnal discharge fluctuations during summer and long-lasting discharge peaks during autumn and winter. Modelling results revealed that bank storage increased with river wave amplitude, wave duration and smaller slope of the river bank, while maximum exchange flux decreased with wave duration. When a homogeneous clogging layer covered the entire river-aquifer interface, hydraulic conductivity positively affected bank storage. The presence of a clogging layer with hydraulic conductivity < 0.001 m d(-1) significantly reduced the exchange flows and virtually eliminated bank storage. The bank storage return/fill time ratio was positively related to wave amplitude and the hydraulic conductivity of the interface and negatively to wave duration and bank slope. Discharge oscillations with short duration and small amplitude decreased bank storage and, therefore, the hyporheic exchange, which has implications for solute fluxes, redox conditions and the potential of riverbeds as fish-spawning locations. Based on these results, river regulation strategies can be improved by considering the effect of certain wave event configurations on hyporheic exchange to ensure harmonious hydrogeochemical functioning of the river-aquifer interfaces and related ecosystems.