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Abstract We investigate the occurrence of anomalous (non‐Fickian) transport in an hydrological catchment system at kilometer scales and over a 36‐year period. Using spectral analysis, we examine the fluctuation scaling of long‐term time series measurements of a natural passive tracer (chloride), for rainfall and runoff. The scaling behavior can be described by a continuous time random walk (CTRW) based on a power‐law distribution of transition times, which indicates two distinct power‐law regimes in the distribution of overall travel times in the catchment. The CTRW provides a framework for assessing anomalous transport in catchments and its implications for water quality fluctuations.