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A chemically patterned microfluidic paper-based analytical device (C-µPAD) is developed to create fluidic networks by forming hydrophobic barriers using chemical vapor deposition (CVD) of trichlorosilane (TCS) on a chromatography paper. By controlling temperature, pattern size, and CVD duration, optimal conditions were determined by characterizing hydrophobicity, spreading patterns, and flow behavior on various sized fluidic patterns. With these optimal conditions, we demonstrated glucose assay, immunoassay, and heavy metal detection on well-spot C-µPAD and lateral flow C-µPAD. For these assays, standard curves showing correlation between target concentration and gray intensity were obtained to determine a limit of detection (LOD) of each assay. For the glucose assays on both well-spot C-µPAD and lateral flow C-µPAD, we achieved LOD of 13 mg/dL, which is equivalent to that of a commercial glucose sensor. Similar results were obtained from tumor necrosis factor alpha (TNFα) detection with 3 ng/mL of LOD. For Ni detection, a colorimetric agent was immobilized to obtain a stationary and uniform reaction by using thermal condensation coupling method. During the immobilization, we successfully functionalized amine for coupling the colorimetric agent on the C-µPAD and detected as low as 150 μg/L of Ni. These C-µPADs enable simple, rapid, and cost-effective bioassays and environmental monitoring, which provide practically relevant LODs with high expandability and adaptability.