Harmful cyanobacteria and their metabolites often contaminate drinking water resources, and effective control remains challenging. Here, we developed a physical algal pre-treatment method, the vertical weir curtain (VWC), to mitigate cyanobacteria and some of their metabolites (geosmin, 2-methylisoborneol (2-MIB), and microcystins) in situ and evaluated its performance in a raw water reservoir used for drinking water supply. The VWC was manufactured with two fibrous polypropylene mats (0% and 92% porosity) which were mounted to maintain a constant underwater depth. We installed the VWC to cover the entire epilimnion of the drinking water intake zone and monitored its efficiency during an algal bloom period (July–October 2015). Reduction rates were 40–59% for total algae, 60–75% for cyanobacteria, 23–55% for geosmin, 30–51% for 2-MIB, and 47–89% for microcystin-LR during the study period. Significant reductions were observed in the shallow layer of the water column (1–3 m water depth), particularly during August, when cyanobacterial density was the highest. The results indicate that the VWC can effectively mitigate harmful cyanobacteria and their metabolites when suitably applied, serving as a valuable reference for the algal reduction in raw drinking water resources.