Currently, many kinds of pesticides in drinking water have listed up in water quality management of Japan, but some pesticides among these compounds were not clear for their analytical procedures. This paper describes the analytical methods for targeted pesticides in aqueous samples, based on their physiochemical properties such as octanol/water partition coefficients (log Pow) and chemical forms at different pH values (pKa and pKb) in water. These values could be employed in liquid-liquid extraction and solid-phase extraction of targeted pesticides from water samples to eliminate contaminants and to extract the compounds. The use of gas chromatography/mass spectrometry (GC/MS, GC/MS/MS), liquid chromatography/mass spectrometry (LC/MS, LC/MS/MS) are more elevated accuracy and selectivity during pesticide analysis in water layers.