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Hydropeaking causes unnatural flow and water level fluctuations in the riparian zone. Biological processes in the riparian zone, such as nutrient cycling, are affected by changes in temperature, oxygen, and moisture, which are all to some extent influenced by the water level. Here, we studied the relationship between hydropeaking and decomposition of organic matter in the riparian zone. Specifically, we measured the decomposition rate (k) and decomposition endpoint (the stabilization factor, S), and examined associations between k, S, hydropeaking, and different environmental variables. Decomposition was estimated using the Tea Bag Index at 33 sites in Swedish rivers and streams with different degrees of hydropeaking. Rivers and streams were sampled in the summer of 2020 (N = 26) and autumn of 2023 (N = 16), with nine sites sampled on both occasions. In summer 2020, k was negatively related to high hydropeaking intensity, but there was no effect of hydropeaking on S. In autumn 2023, there was no effect of hydropeaking on k or S. Of the other environmental variables tested (substrate grain size, temperature, and length of growing season), the growing season had a positive relationship with S in autumn 2023. Our findings indicate that reducing hydropeaking during summer, when biological activity is high, may be beneficial for maintaining riparian function.