The paper presents quantitative changes of selected 2- and 3-ring PAHs after process phases of GSBR reactor. The studies have been carried out for 264 cycles of GSBR reactor, during which concentration of naphthalene was increased in the range of 3.00–710.00 μg/L, acenaphthylene 1.00–160.00 μg/L, acenaphthene 3.00–440.00 μg/L. GSBR operating cycle consisted of filling (30 min), mixing (90 min), aeration (540 min), sedimentation (10 min), decanting (30 min) and downtime (20 min) phases. Activated sludge dry mass concentration was 4.00 kg/m3. Conducted studies showed that in GSBR reactor naphthalene was degraded with the highest intensity. Results of the statistical analysis confirmed that naphthalene concentrations were statistically significantly different (α = 0.05) after each individual GSBR process phase, while in case of acenaphthene and acenaphthylene, the differences were observed only between mixing and aeration phases. Additionally, equations estimating concentrations of PAHs in treated wastewater were developed. Selected activated sludge technological parameters (sludge volume index, sludge and hydraulic retention time) and concentration of PAHs were used for equations. The R2 coefficients of equations were above 0.99, which indicates a good adjustment of estimation to observed values.