City governments are currently exploring different participatory mechanisms in order to meet the growing demand in society for deliberate decision-making. Through developments in sensing technology, data processing and visualization, citizen science is emerging as a powerful tool for the general public to participate in scientific research that informs policy. Citizen science can be used as an approach in Urban Living Labs, whereby public and private stakeholders are involved in innovation and data collection processes together with citizens. However, there is currently little synergy between citizen science and Urban Living Labs, and how science, innovation and policy can be interoperable. Therefore, this article conducts a comparative case study analysis on the participatory processes and related outputs, outcomes and impacts of the FloodCitiSense Urban Living Labs (Brussels, Birmingham, Rotterdam). These initiatives developed an early warning system for urban flooding through the collection and analysis of crowdsourced information. Data on the participatory processes were collected through 11 in-depth interviews and evaluated on its effectiveness in achieving policy outcomes. The discussion reflects on best practices in incorporating citizen science in Urban Living Labs based on the experienced opportunities and challenges in FloodCitiSense.