Abstract Alteration in the river flow regime due to intermittent hydropower production (i.e., hydropeaking) leads to biodiversity loss and ecosystem degradation worldwide. Due to the increasing shear of volatile green energy (i.e., wind and solar), hydropeaking frequency is deemed to increase in the coming decades. However, our mechanistic understanding of how the frequency of repeated hydropeaking (i.e., series of multiple events) affects ecological processes is still limited. Here, we reflect on the impacts of altered flow frequency and relative duration on the persistency of aquatic habitats. We focus on the habitats at patch‐scale, being this the scale representing what organisms perceive when interacting with their environment. With a showcase we explore a temporally explicit approach to quantify altered habitat dynamics at patch‐scale due to hydropeaking. We then review how changes in habitat dynamics and persistency may affect ecological processes. Our findings suggest that (i) a time‐series approach allows to account for the inherent multi‐event nature of hydropeaking; (ii) hydropeaking can increase the dynamics of single habitat patches by at least one order of magnitude if compared to unregulated rivers; (iii) altered habitat dynamics at the patch scale can affect the survival of more sessile species and life cycle stages (e.g., invertebrates) or the energy budget of mobile species and life cycle stages (e.g., adult fish). However, the ecological significance and potential environmental thresholds of patch‐scale dynamics and persistency are still poorly investigated and need further attention. Moreover, methods for the aggregation of habitat dynamics and persistency from the patch to the reach‐scale are not available yet.