Bank filtration (BF) is an established indirect water-treatment technology. The quality of water gained via BF depends on the subsurface capture zone, the mixing ratio (river water versus ambient groundwater), spatial and temporal distribution of subsurface travel times, and subsurface temperature patterns. Surface-water infiltration into the adjacent aquifer is determined by the local hydraulic gradient and riverbed permeability, which could be altered by natural clogging, scouring and artificial decolmation processes. The seasonal behaviour of a BF system in Germany, and its development during and about 6 months after decolmation (canal reconstruction), was observed with a long-term monitoring programme. To quantify the spatial and temporal variation in the BF system, a transient flow and heat transport model was implemented and two model scenarios, ‘with’ and ‘without’ canal reconstruction, were generated. Overall, the simulated water heads and temperatures matched those observed. Increased hydraulic connection between the canal and aquifer caused by the canal reconstruction led to an increase of ~23% in the already high share of BF water abstracted by the nearby waterworks. Subsurface travel-time distribution substantially shifted towards shorter travel times. Flow paths with travel times <200 days increased by ~10% and those with <300 days by 15%. Generally, the periodic temperature signal, and the summer and winter temperature extrema, increased and penetrated deeper into the aquifer. The joint hydrological and thermal effects caused by the canal reconstruction might increase the potential of biodegradable compounds to further penetrate into the aquifer, also by potentially affecting the redox zonation in the aquifer.