Steroid estrogens namely 17β-estradiol (E2) and 17α-ethinylestradiol (EE2) and antibiotics including sulfamethoxazole (SMX) are pharmaceutically active compounds (PhAC) of emerging concern due to their environmental and human health impacts even at ppb range concentrations. These compounds usually flow to wastewater treatment plants (WWTP) and are released to the aquatic systems due to inefficient removal in conventional biological systems. In this work, a sequencing batch reactor (SBR) with aerobic granular sludge (AGS) was operated in the presence of E2, EE2 and SMX. SVI 5 , SVI 30 /SVI 5 ratio, VSS, and TSS of mature AGS (in absence of PhAC), as well as in the presence of PhAC (0.221 mg L − 1 of E2, 0.278 mg L − 1 of EE2 and 0.290 mg L − 1 of SMX), were successfully predicted with multilinear regression (MLR) using morphological and structural parameters of floccular and granular fractions of AGS obtained from quantitative image analysis (QIA). Good prediction models were obtained for the SVI 5 (R 2 of 0.976), floccular VSS (R 2 of 0.949) and TSS (R 2 of 0.934), granular VSS (R 2 of 0.930) and TSS (R 2 of 0.916), SVI 30 /SVI 5 ratio (R 2 of 0.917) and density (R 2 of 0.889). These results emphasize the usefulness of this methodology for monitoring dysfunctions in AGS in the presence of the studied PhAC.