In this work, a method for mercury speciation using magnetic nanoparticles (MNPs) coated with dithiol and detection by cold vapor atomic fluorescence spectrometry (CV AFS) was developed. The magnetic Fe3O4 nanoparticles were coated with Al2O3 and sodium dodecyl sulfate (SDS) and functionalized with 1,3,4-thiadiazole-2,5-dithiol (TDT). The resulting functionalized MNPs (FMNPs, Fe3O4@Al2O3-TDT) were dispersed in the water samples, and the sorption performance with different mercury species was investigated. Once retained on the surface of Fe3O4@ Al2O3-TDT MNPs, the mercury species were magnetically separated from the sample and eluted with HCl. The organic mercury species were oxidized employing KBr-KBrO3 (100 and 17 mM, respectively) in an acid medium (HCl 1.0 M), and the results were expressed considering the total inorganic mercury concentration. It was successfully applied in mercury speciation analysis in the estuarine water, followed by CV AFS determination. In the proposed method under optimal conditions (pH 6), inorganic mercury was quantified in a linear range from 10 to 2000 ng L−1, with a limit of detection of 0.55 ng L−1, relative standard deviation (RSD) < 1.62%, and an enrichment factor of twelve. The recoveries in spiked estuarine water samples ranged from 94 to 106% for Hg(II), 85–91% for MeHg, 83–94% for EtHg, and 84–95% (PhHg) using two levels of concentration (100 and 500 ng L−1). The method is accurate, precise, and efficiently applied in mercury species determination in a complex matrix without laborious and time-consuming sample preparation.