The method employing molecularly imprinted polymers for the extraction and clean up of endocrine-disrupting compounds (estrogens, bisphenol A, and alkylphenols) from water and sediment is described. The identical extraction/clean-up and LC-MS/MS condition were used for the analysis of both types of samples. The method showed high recoveries ranging from 90 to 99% with excellent precision (intrabatch: 3.6–9.3%; interbatch: 5.6–11.4% for water; intrabatch: 4.3–8.5%; interbatch: 6.1–9.6% for sediment). The LOD was in the range of 0.7–1.9 ng/L and 0.3–0.6 ng/g for water and sediment, respectively. Overall extraction on molecularly imprinted polymers substantially enhanced sample clean-up. The difference in efficiency of clean-up was particularly pronounced when a large sample volume/weight was extracted and analyzed. Finally, the method was successfully applied for the analysis of 20 water and sediment samples.