A cross-linked methacrylate molecularly imprinted polymer (poly-4-vinylpyridine-co-trimethylolpropane-trimethacrylate) selective for bisphenol A (BPA) was synthesized, using a fluorinated BPA derivative (4,4'-(hexafluoroisopropylidene)-diphenol) as a mimic template, and applied to the analysis of real-world samples of process and potable waters. The molecularly imprinted polymer also showed a high affinity and selectivity for 17-beta-estradiol and ethynylestradiol. A method to analyze BPA, 17-beta-estradiol, and ethynylestradiol at ultratrace levels was thus developed from a screening procedure to monitor endocrine-disrupting chemicals in water samples. The method consists of the BPA-selective cleanup by molecularly imprinted SPE using cartridges packed with the polymer developed, its recovery by stir bar sorptive extraction after ad hoc derivatization to obtain the corresponding BPA-acetate, and its analysis by GC-time window-SIM-MS after online thermal desorption. The method showed good linearity in the working range (R(2)=0.9969), high repeatability (RSD% <10.1), recoveries always above 90%, and very low LOD (10 pg/L) and LOQ (1 ng/L) and can easily be extended to the determination of 17-beta-estradiol and ethynylestradiol ultratraces. The method's effectiveness was evaluated by analyzing the real-world water samples; it enabled preconcentration and detection of BPA at ultratrace levels.