Abstract. Transition from endorheic alluvial fan environments to well-channelized fluvial systems in natural conditions may occur in response to base-level fluctuations. However, human-induced changes in semi-arid regions can also be responsible for similar unforeseen modifications. Our results confirm that in-channel gravel mining and aquifer overexploitation over the last 50 years in the case study area have changed the natural stability of the Nogalte stream and, as a result, its geomorphic parameters including channel depth and longitudinal profile have begun to adapt to the new situation. Using interferometric synthetic aperture radar (InSAR) data we obtain maximum values for ground subsidence in the Upper Guadalentín Basin of ∼ 10 cm yr−1 for the period 2003–2010. In this context of a lowered base level, the river is changing its natural flood model to a more powerful one. A comparison of the 1973 flood event, the most dramatic flood event ever recorded in the area, with the 2012 event, where there was a similar discharge but a sediment load deficit, reveals greater changes and a new flooding pattern and extension. In-channel gravel mining may be responsible for significant local changes in channel incision and profile. This, together with the collateral effects of aquifer overexploitation, can favour increased river velocity and stream power, which intensify the consequences of the flooding. The results obtained here clearly demonstrate an existing transition from the former alluvial pattern to a confined fluvial trend, which may become more pronounced in the future due to the time lag between the drop in aquifer level and ground subsidence, and introduce a new scenario to be taken into consideration in future natural hazard planning in this area.