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Aedes and Culex mosquitoes, known for spreading arboviruses like dengue and West Nile, thrive in cities, posing health risks to urban populations. Climate change can create suitable climatic conditions for these vectors to spread further in Europe. Cities contain numerous landscape and infrastructure elements, such as storm drains, that allow stagnant water build-up facilitating mosquito breeding. Modifying urban infrastructure to prevent water accumulation can reduce mosquito populations, but evidence is limited. The Public Health Agency of Barcelona, Spain, introduced a structural modification of storm drains to prevent water accumulation. Together with the Agency, we designed a randomised controlled trial (RCT) to experimentally assess the effectiveness of these modifications on adult Aedes albopictus and Culex pipiens populations. It is a parallel-arm RCT with equal randomization of 44 drains to receive mosquito-proofing modifications (intervention) or not (control). Primary outcomes are adult mosquito counts and secondary outcomes are larvae and mosquito presence, assessed weekly at each drain until no mosquitoes are detected. Data analyses include generalised linear mixed models to estimate the time-averaged and highest intervention effects, subgroup and sensitivity analyses. The trial results will guide a city-wide expansion of the storm drain modifications and provide valuable evidence to enhance existing vector control measures.