A number of analytical methods have been developed in the past few years for environmental monitoring of plutonium (Pu) isotopes around nuclear facilities within protocols for emergency preparedness as well as for risk assessment of contaminated areas resulting from nuclear weapon tests, nuclear accidents, and the discharge of nuclear waste. This article summarizes and critically compares recently reported methods for determination of Pu isotopes in waters and environmental solid substrates, in which sample pre-treatment is imperative for separation of the target species from matrix ingredients and/or potentially interfering nuclides prior to detection by radiometric or mass spectrometric techniques. Also discussed, via representative examples, is the automation of the entire analytical protocol by on-line extraction chromatography and ion exchange chromatography using flow injection (FI) or sequential injection (SI) approaches.