This study aimed to investigate the ability of analyte protectants to enhance GC-MS signals and compensate matrix effects for a range of micropollutants in pure standard, effluent, and influent wastewater samples during analysis and detection. Wastewater samples were prepared for analysis using multilayer solid phase extraction for the purpose of extracting sample components with a broad range of physical-chemical properties. The sample extracts were either spiked or not spiked with target compounds and four analyte protectants: 3-ethoxy-1,2-propanediol, D-sorbitol, gluconolactone, and shikimic acid. In this way, it was possible to evaluate the matrix effects of wastewater samples and compare the use of analyte protectants with the conventional correction method of allocating a best matching internal standard to each target compound. A relation was observed between level of wastewater treatment and matrix effects, with the largest effects observed for influent samples and the smallest effects for effluent samples. Compensation of matrix effects with analyte protectants gave comparable results with the conventional correction method of allocating a best matching internal standard to each of the 13 investigated micropollutants. The best overall compensation was observed using analyte protectants and the internal standard correction method in combination.