The introduction of invasive fish species to aquatic ecosystems has been demonstrated to cause disastrous ecological effects. Current conservation strategies regard rotenone-containing piscicide formulations, such as commercial product CFT Legumine, as a potentially viable alternative to the cumbersome traditional approaches to fish eradication. This consideration relies on the fast degradation of rotenone and its relatively rapid dissipation from the environment. Piscicide treatments in fragile aquatic ecosystems should thus monitor not only rotenone concentrations following application, but also other byproducts and degradation products. We present a methodology for the analysis of rotenoids in fresh and brackish waters that addresses two main challenges: the accurate determination of applied concentrations in different salinity concentrations by performing a simplified on-site solid-phase extraction, overcoming the fast degradation of rotenone in sample storage conditions, and the selective analysis of rotenoid byproducts and degradation products by gas chromatography coupled to mass spectrometry. Limits of quantification were below the ecological no-effect concentration of rotenone (2 µg/L) and average recoveries exceeded 80%. Accuracy (compared to expected values) and precision (deviation of replicates) ranged from 78 to 103% and 3 to 14%, respectively, across various rotenoid concentrations. These metrics are more than satisfactory for the intended application of this simplified procedure. The method was applied to piscicide-treated samples, revealing significant and fast degradation of parent rotenoids in storage conditions, as well as a non-negligible accumulation of rotenone in the particulate fraction of water that could impact the effectivity of eradication efforts.