A borehole is drilled from the surface to an underground shale matrix. A pipe is inserted into the borehole. Openings are created in the pipe in fluid communication with fractures in the shale matrix. The interior surface of at least one section of pipe is coated with a contaminant-capturing substance. Fracturing fluid including water, proppants and chemicals is pumped through the pipe and into the fractures in the shale matrix. The fluid re-enters the pipe from the shale matrix and moves toward the surface through the coated pipe section where contaminants are sequestered by the coating. Natural gas or oil from the fractured shale then enters the pipe and moves to the surface to be collected. The coated pipe section remains in the ground permanently such that the necessity of disposing of the captured contaminants is eliminated.