A method for measuring the Brillouin shift in water is investigated. It is based on the technique of the filters with resonant absorption of molecules. By using the two symmetric absorption peaks of iodine molecules within the frequency range of Brillouin scattering in water, accurate real-time measurement of Brillouin shift in water could be achieved. The principle of the technique is analyzed and a real system which can be used in practical applications is given. Also, the inherent errors and the sensitivity for measuring of the system are discussed. The experimental results using this method are given. It shows that this method has several advantages such as good real-time measurement, high sensitivity, high precision compared to the classical technique such as using Fabry-Perot.