Herein we report fabricating a microfluidic device to monitor harmful algal blooming (HAB). The heterogeneous immuno-enzyme assay was integrated into a self-designed microfluidic chip for rapid and automatic analysis of algal toxins. The device was made from polydimethylsiloxane (PDMS) and was assembled with a home-made control system. The performance of the system was demonstrated by the detection of microcystin, saxitoxin and cylindrospermopsin, the major cyanotoxins. In one single microfluidic chip, multiple samples were controlled and analysed in a parallel manner. Under the optimal conditions, the linear range and the limit of detection of microcystins were 0-5.0 ng mL(-1) and 0.02 ng mL(-1) respectively. The total analysis time was less than 25 min. The designed device was highly automatic, more efficient and economic compared to conventional techniques.