A method for determination of polyorganosiloxanes (by silicon) in water using high-resolution continuum source electrothermal atomic absorption spectrometry with the preliminary extraction of the analytes from the analyzed sample by benzene is proposed. The parameters of the time–temperature program of an atomizer are optimized using a storm water sample. To eliminate chemical interference during the determination of silicon, graphite cuvettes have been modified with a permanent modifier (sodium tungstate) to form a carbide coating. The thermal stabilization of silicon in a graphite furnace has been achieved in the presence of a mixed palladium–magnesium modifier in the nitrate form. The developed method of analysis has been used to determine the content of polyorganosiloxanes (by silicon) in natural water samples. The metrological characteristics of the method in the determined silicon content range of 0.01–100 mg/dm3 have been estimated.