Herein, some (modified) paper–based substrates were prepared and utilized as extractive phases in a microfluidic device and their extraction performances examined for analytes with different polarities. Reagents including hexadecyltrimethoxysilane (HDTMS), phenyltrimethoxysilane (PTES), (3-aminopropyl) triethoxysilane (APTES) and 3–(2,3–epoxypropoxy) propyltrimethoxysilane (EPPTMOS) were implemented for the modification process. Due to the induction of different silane functional groups, it was anticipated to have various interactions for the tested analytes. Eventually, the prepared paper sheets were used as extractive phases for solid–phase extraction within a microfluidic system. The microfluidic setup not only improves the mechanical stability of the paper–based phases but also facilitated the mass transfer process and decreases the energy consumption. The selected analytes contained antidepressant drugs, organophosphates and triazine toxins, having different structures and polarities. Afterward, the existing interactions between the paper–based sorbents and the selected analytes were investigated by Principal Component Analysis (PCA) and Hierarchical Clustering Analysis (HCA) for data analysis. According to the obtained data, the PTES modified surface paper was selected for quantitative investigation and optimization. The major parameters associated with the extraction performance were studied. A linear range was obtained for amitriptyline and trimipramine, 0.05–200 μg L−1, and the calibration graph for clomipramine was linear in the range of 0.02–200 μg L−1. The employment of microfluidic device in conjunction with gas chromatography-mass spectrometry led to the limits of detections of 0.005–0.01 μgL−1 for the antidepressant drugs. The relative recoveries for the tested drugs in urine samples were in the range of 95–103%.