Immunoagglutination assay is a promising approach for the detection of waterborne analytes like virus, cells, proteins with its advantages such as a smaller amount of reagents and easier operation. This paper presents a microfluidic agglutination assay on which all the assay processes including analyte capture, agglutination, and detection are performed. The chip integrates an on-chip pump for sample loading, a dynamic magnetic bead (MB) clump for analyte capture and agglutination, and a sheath-less flow cytometry for particle detection, sizing, and counting. The chip is tested with streptavidin-coated MBs and biotinylated bovine serum albumin as a model assay, which realizes a limit of detection (LOD) of 1 pM. Then, an antigen/antibody assay using rabbit IgG and goat anti-rabbit IgG coated MBs is tested and a LOD of 5.5 pM is achieved. At last, human ferritin in 10% fetal bovine serum is tested with Ab-functionalized MBs and the detection achieves a LOD of 8.5 pM. The whole procedure takes only 10 min in total.