AbstractIn addition to a rise in mean air and water temperatures, more frequent and intense extreme climate events (such as heat waves) have been recorded around the globe during the past decades. These environmental changes are projected to intensify further in the future, and we still know little about how they will affect ecological processes driving harmful cyanobacterial bloom formation. Therefore, we conducted a long‐term experiment in 400‐L shallow freshwater mesocosms, where we evaluated the effects of a constant +4°C increase in mean water temperatures and compared it with a fluctuating warming scenario ranging from 0 to +8°C (i.e., including heat waves) but with the same +4°C long‐term elevation in mean water temperatures. We focused on investigating not only warming effects on cyanobacterial pelagic dynamics (phenology and biomass levels), but also on their recruitment from sediments—which are a fundamental part of their life history for which the response to warming remains largely unexplored. Our results demonstrate that (1) a warmer environment not only induces a seasonal advancement and boosts biomass levels of specific cyanobacterial species in the pelagic environment, but also increases their recruitment rates from the sediments, and (2) these species‐specific benthic and pelagic processes respond differently depending on whether climate warming is expressed only as an increase in mean water temperatures or, in addition, through an increased warming variability (including heat waves). These results are important because they show, for the first time, that climate warming can affect cyanobacterial dynamics at different life‐history stages, all the way from benthic recruitment up to their establishment in the pelagic community. Furthermore, it also highlights that both cyanobacterial benthic recruitment and pelagic biomass dynamics may be different as a result of changes in the variability of warming conditions. We argue that these findings are a critical first step to further our understanding of the relative importance of increased recruitment rates for harmful cyanobacterial bloom formation under different climate change scenarios.