Application of selenium nanoparticle (SeNP)-based fertilizers results in the release of SeNPs to aquatic systems, where SeNPs may transform into inorganic selenite (Se(IV)) and selenate (Se(VI)) with higher toxicity. However, methods for the speciation analysis of different Se species are lacking, hindering the accurate assessment of the risks of SeNPs. Herein, for the first time, a Triton X-45 (TX-45)-based dual-cloud point extraction (CPE) method was established for the selective determination of SeNPs, Se(IV), and Se(VI) in water. TX-45 can adsorb on the surface of SeNPs and facilitate the extraction of SeNPs into the lower TX-45-rich phase in the first CPE, while Se(VI) and Se(IV) retain in the upper aqueous phase. In the second CPE, Se(IV) can selectively associate with diethyldithiocarbamate and be concentrated in the TX-45-rich phase, whereas Se(VI) remains in the upper phase. Different Se species can be isolated and then quantified by ICP-MS. The presence of coexisting ions and dissolved organic matter (0−30 mg C/L) did not interfere with extraction and separation. The feasibility of the presented method was confirmed by the analysis of natural water samples, with a detection limit of 0.03 μg/L and recoveries in the ranges of 61.1−104, 65.5−113, and 80.3−131% for SeNPs, Se(IV), and Se(VI), respectively. This study aims to provide an effective method to track the fate and transformation of SeNPs in aquatic systems and further contribute to estimating the potential risks of SeNPs to environmental organisms and human bodies.