Pesticides are among the most detected contaminants in the aquatic environment. This is mainly due to their use in agriculture and their physico-chemical properties that enable transportation and a persistent or pseudo-persistent existence in the water media. Several directives and guidelines set maximum levels of pesticides in water in order to protect the human and environmental health. A brief discussion of the existing directives and guidelines concerning pesticides in water is presented, e.g., the new regulatory framework for the Registration, Evaluation and Authorisation of Chemicals (REACH), and the Directive 91/414/EEC concerning the placing of plant protection products on the market. Up-to-date analytical tools to support the REACH program are of prime importance to ensure its complete implementation. Since liquid chromatography (LC) coupled to mass spectrometry (MS) is considered the most appropriate technique for determination of most modern pesticides in environmental waters, the most recent developments and applications in this field are discussed in detail in this review.