Establishing rapid, simple, and in situ detection of microcystin-LR (MC-LR) in drinking water sources is of significant importance for human health. To ease the situation that current methods cannot address, an open surface droplet microfluidic magnetosensor was designed and validated to quantify MC-LR in reservoir water, which is capable of (1) MC-LR isolation via MC-LR antibody-conjugated magnetic beads, (2) parallel and multistep analytical procedures in 15-array power-free and reusable active droplet microfluidic chips, (3) immunoassay incubation and fluorescence excitation within a miniaturized multifunctional 3D-printing optosensing accessory, and (4) signal read-out and data analysis by a user-friendly Android app. The proposed smartphone-based fluorimetric magnetosensor exhibited a low limit of detection of 1.2 × 10-5 μg/L in the range of 10-4 μg/L to 100 μg/L. This integrated and high throughput platform was utilized to draw an MC-LR contamination map for six reservoirs distributed in the Pearl River delta, Guangdong Province. It promises to be a simple and successful quantification method for MC-LR field detection, bringing many benefits to rapid on-site screening.