Because of their predetermined selectivity, molecularly imprinted polymers (MIPs) have been extensively investigated to offer efficient separation of organic pollutants for water analysis and purification. In this review, we first describe the current development of water compatible MIPs, and the physical encapsulation and chemical immobilization of MIP particles for practical applications related to water analysis and purification. We summarize the challenges in understanding the mechanisms in molecular imprinting, with a special emphasis on the use of nuclear magnetic resonance (NMR), dynamic light scattering (DLS), and synchronous fluorescence spectroscopy to gain theoretical insights into the molecular imprinting process. The highlighted synthetic methods and the mechanistic investigations discussed in this review should facilitate the identification of the most crucial factors affecting the applications of MIPs for clean water.