Reports on the determination of emerging contaminants (EC) in aqueous samples have been increasingly common. Due to the low levels of concentration of the analytes as well as the complexity of this matrix, the analysis is done preferably by liquid chromatography (LC). Owing to the polar character of most of the EC determination by gas chromatography is deprecated. One way to overcome this barrier is through derivatization, which, in some cases, can be a lengthy step, presents risks to the analyst as well as to the environment due to the toxicity of the derivatizing agent, and, thus, ends up favoring the use of LC. An analytical protocol was developed in this work to increase the efficiency of derivatization in a shorter reaction time for the determination of ibuprofen, 4-octylphenol, 4-nonylphenol, triclosan, bisphenol A, diclofenac, estrone, 17-β-estradiol, estriol, coprostanol, and cholesterol. The proposal then was to carry out the silylation reaction of the analytes with the aid of a domestic microwave oven. The results indicated that the use of the device provided an increase in the efficiency of the reaction, due to the homogeneous heating of the solution. Besides, there was a significant decrease in the derivatization time of the analytes from 30 min to 5 min. Additionally, through a design of experiments (DOE), it was possible to perceive the influence of some instrumental parameters of GC-MS, such as temperature, pressure intensity, and pressure pulse time in the injector on the detectability of the investigated analytes. This study allowed a satisfactory separation of the analytes and an average increase in their areas of up to 35%. These aspects made it possible to obtain an analytical method with limits for the detection and quantification of EC between 0.03-11.00 ng mL-1 and 0.10-33.35 ng mL-1, respectively, and uncertainties below 9%. The developed method was applied in the determination of the analytes in coastal seawater and the determined concentrations varied from 0.24 ng L-1 for estriol and 43.60 ng L-1 for cholesterol. Thus, the improvement of the silylation reaction, combined with the strategy of instrumental optimization, proved to be simple, efficient, and fast, as well as being a comparable alternative to liquid chromatography.