Catchment-wide denudation rates (CWDRs) obtained from cosmogenic nuclides are an efficient way to determine geomorphic processes quantitatively in alpine mountain ranges over Holocene time scales. These rate estimations assume steady geomorphic processes. Here we use a time series (3 yr) in the Aare catchment (central Swiss Alps) to test the impact of spatially heterogeneous stochastic sediment supply on CWDRs. Our results show that low-frequency, high-magnitude debris-flow events significantly perturb cosmogenic nuclide (10Be, 14C) concentrations and thus CWDRs. The 10Be concentrations decrease by a factor of two following debris-flow events, resulting in a doubling of inferred CWDRs. The variability indicates a clear time and source dependency on sediment supply, with restricted area-weighted mixing of sediment. Accordingly, in transient environments, it is critical to have an understanding of the history of geomorphic processes to derive meaningful CWDRs. We hypothesize that the size of debris flows, their connectivity with the trunk stream, and the ability of the system to sufficiently mix sediment from low- and high-order catchments control the magnitude of CWDR perturbations. We also determined in situ 14C in a few samples. In conjunction with 10Be, these data suggest partial storage for colluvium of a few thousand years within the catchment prior to debris-flow initiation.