Environmental pollutants that disrupt endocrine functions, such as natural and synthetic estrogens, can significantly compromise the ecological and biological balance of ecosystems, in particular aqueous habitats. Long-term exposure to endocrine disruptors has adverse effects on water organisms and, consequently, humans. In nature, estrogens occur at very low concentrations, and their presence in environmental samples is very difficult to confirm. Selective and repeatable methods for preparing aqueous samples and reliable separation and identification techniques are required to accomplish the above task. Molecularly imprinted solid-phase extraction (MISPE) polymers are popularly used for the preparation of water samples. This article overviews the existing knowledge about sample preparation methods, with special emphasis on the progress made in the synthesis of molecularly imprinted polymers as effective sorbents for isolating estrogens from environmental and biological samples. The latest technological solutions, including molecularly imprinted polymer nanoparticles, are discussed as potential methods for isolating selected analytes. The challenges and prospects associated with new selective sorbents are also discussed.