Display omitted •Development of a flow microdevice with programmable in situ hydrogel formation.•Utilization of Fe-alginate hydrogel as the electric stimuli-responsive material.•On-demand release of Fe2+ ions for controlled reactive radical formation.•Portable microfluidic device for continuous BPA degradation at the pollution source.•Model-based design for iterative optimization and process intensification. An innovative electrochemical microreactor leveraging redox-responsive hydrogels for the targeted removal of organic pollutants has been presented in this study. The centrepiece is a redox-responsive alginate hydrogel cross-linked with iron ions, capable of controlling the release of Fe ions by an external electrical stimulus. The Fe ions were used to activate persulfate, leading to the formation of reactive sulfate and hydroxyl radicals in situ. The system was tested for the continuous degradation of organic pollutants by radical oxidation using bisphenol A (BPA) as a model system. This unique, responsive feature of the alginate hydrogel enables its modulation and thus the removal of BPA on demand. In continuous operation, a BPA removal efficiency of over 94 % was achieved, demonstrating the enormous potential of microfluidic setup for the environmental remediation of various organic pollutants. By tailoring the process conditions, such as the residence time, even a complete removal of BPA was achieved. The robust and portable design should enable the utilization of such a system at the site of contamination. Due to the efficient process control achieved through microfluidic design, the study further delves into the adaptability of this system to different environmental matrices and showcases its potential as a promising solution to the increasing global threat of water pollution. Thereby, this research opens up new strategies for niche-oriented pollution management, including model-based design approaches. The CFD model was applied to simulate and optimize process conditions, enabling further process intensification.