Two complementary LC-MS ionization methods, electrospray (ESI) and atmospheric pressure photoionization (APPI), have been optimized to determine three natural estrogenic compounds (estrone, 17beta-estradiol and estriol) and two synthetic estrogenic compounds (17alpha-ethynylestradiol and diethylstilbestrol) in the influent and effluent of wastewater treatment plants (WWTPs). The wastewater samples were first subjected to solid-phase extraction coupled with desalting extraction to remove matrix interference. The analytes were then detected using liquid chromatography-tandem mass spectrometry (LC-MS-MS) with ESI and dopant-assisted (DA) APPI to evaluate the ion suppression effect and to complement the detection and quantification of estrogenic compounds in complex wastewater samples. The average ion suppression factors for the extracts of the WWTP influent analyzed using ESI and APPI were 52+/-5% and 27+/-7%, respectively. The sensitivity and ionization efficiency of the LC-ESI-MS-MS system decreased dramatically when a complex matrix was present in the WWTP influent sample. Estrogenic compounds could be detected in the WWTP influent and effluent samples at concentrations below the parts-per-billion level. The lower detection limits obtained when using ESI and the higher matrix tolerance of the APPI method allowed the complete quantification of estrogenic compounds in very complex samples in a complementary manner.