The frequency of abnormally warm water events is increasing not only in surface waters, but also in subsurface layers, with major impacts on benthic ecosystems. Previous insights on heatwave effects have been obtained through field observations or manipulative laboratory experiments. Here, we introduce a system capable of inducing elevated water temperatures in benthic habitats in situ over several days. The system consists of a commercially available electric boiler, usually applied in domestic underfloor heating, and custom‐designed benthic acrylic glass chambers connected to individual thermostats. Furthermore, the chambers are semi‐open, allowing constant water exchange, maintaining otherwise near‐natural conditions, including oxygen concentrations, while the temperature is elevated. The water exchange can be stopped to facilitate incubations measuring changes in benthic fluxes. We conducted a 15‐d trial study in July 2021 on a bare‐sediment habitat at 2.5 m depth, exposing five chambers to water temperatures 5°C above ambient temperatures for 6 d and comparing with five control chambers. In this assessment, we demonstrate that the temperature control and stability were reliable while maintaining natural oxygen conditions. The modular character of the system permits adaptations for various benthic habitats, facilitating the investigation of elevated temperatures in situ for future climate change scenarios.