A fast and sensitive analytical procedure has been developed for the simultaneous separation and determination of α-estradiol, β-estradiol, estriol, estrone and ethynylestradiol and their sulfate, glucuronide and acetate conjugates in river sediments. The procedure includes a microwave-assisted extraction (MAE) with aqueous methanol (25:75, v/v) at 100 °C in 10 min, a clean-up on Oasis WAX cartridge and a high-performance liquid chromatography–ion-trap tandem mass spectrometry (HPLC-IT-MS/MS) with electrospray ionization. The recovery for each compounds ranged from 83 to 107% and the repeatability represented as RSDs ranged from 4.9 to 9.6%. The limits of detection (LODs) were down to 1 ng g −1. The analytical performance of the method was evaluated using determination of free and conjugated estrogens in river sediments.