Rapid development and applications of unmanned aerial vehicles (UAVs) provide promising solutions to and new opportunities for environmental monitoring. Owing to their flexibility in flight scheduling, high spatial resolution, and costs-effectiveness, UAVs have become a popular tool for monitoring dynamic environmental processes, such as emergence and outbreak of harmful algae blooms (HABs). The HABs outbreak, often linked with anthropogenic eutrophication, has become a serious environmental health problem that threats our communities. Existing studies show that UAV-based HABs monitoring is a cost-effective means of assisting environmental managers in developing precautionary warning system and coping strategies. This article summarized the state-of-the-art of using UAVs and lightweight onboard multispectral sensors for HABs monitoring from the perspective of quantitative remote sensing. It culminates in a discussion of challenges and opportunities for future research and applications on drone-based HABs monitoring.