We report the development and tests of several systems for the simultaneous determination of 18 energetic compounds and related congeners in untreated water samples. In these systems a Restricted Access Material trap or liquid-chromatography precolumn (with a C(18) or porous graphitic carbon, PGC, stationary phase) followed by a PGC analytical column are used for sample clean-up, enrichment and separation of the trace level analytes, which are then analyzed by mass spectrometry (MS). The relative merits of two MS ionization interfaces (atmospheric pressure chemical ionization, APCI, and atmospheric pressure photoionization, APPI) were also compared for the MS identification and quantification of these analytes. APCI was found to be superior in cases where both alternatives are applicable. A major drawback when applying APPI is that no signal is obtained for the cyclic nitramines and nitrate esters. Using APCI, a wide spectrum of unstable compounds can be determined in a single analysis, and the feasibility of using large volume samples (up to 100 mL) in combination with the sensitivity of the MS detection system provide method detection limits ranging from 2.5 pg/mL (for 2,4-dinitrotoluene and 2,6-diamino-6-nitrotoluene) to 563 pg/mL (for pentaerythritol tetranitrate, PETN), with repeatability ranging from 2 to 7%. Other chemometric parameters such as robustness, selectivity, repeatability, and intermediate precision were also evaluated in the validation of the extraction methods for use in water analysis. Tests with untreated groundwater and drinking water samples, spiked with 20 ng of the analytes, yielded results similar to those obtained with high purity water samples.