Understanding the interplay between hydrological flushing and biogeochemical cycling in streams is now possible owing to advances in high‐frequency water quality measurements with in situ sensors. It is often assumed that storm events are periods when biogeochemical processes become suppressed and longitudinal transport of solutes and particulates dominates. However, high‐frequency data show that diel cycles are a common feature of water quality time series and can be preserved during storm events, especially those of low‐magnitude. In this study, we mine a high‐frequency dataset and use two key hydrochemical indices, hysteresis and flushing index to evaluate the diversity of concentration‐discharge relationships in 3rd order agricultural stream. We show that mobilisation patterns, inferred from the hysteresis index, change on a seasonal basis, with a predominance of rapid mobilisation from surface and near stream sources during winter high‐magnitude storm events and of delayed mobilisation from subsurface sources during summer low‐magnitude storm events. Using Dynamic Harmonic Regression, we were able to separate concentration signals during storm events into hydrological flushing (using trend as a proxy) and biogeochemical cycling (using amplitude of a diel cycle as a proxy). We identified three groups of water quality parameters depending on their typical c‐q response: flushing dominated parameters (phosphorus and sediments), mixed flushing and cycling parameters (nitrate nitrogen, specific conductivity and pH) and cycling dominated parameters (dissolved oxygen, redox potential and water temperature). Our results show that despite large storm to storm diversity in hydrochemical responses, storm event magnitude and timing have a critical role in controlling the type of mobilisation, flushing and cycling behaviour of each water quality constituent. Hydrochemical indices can be used to fingerprint the effect of hydrological disturbance on freshwater quality and can be useful in determining the impacts of global change on stream ecology.