This study demonstrates the application of in situ ferrate (Fe(VI)) for the efficient removal of dissolved algal organic matter (AOM) from seawater. Sodium hypochlorite (NaOCl) and ferric (Fe(III)) were used to produce in situ Fe(VI) by wet chemical oxidation. First, the removal efficiencies of model AOM compounds, humic acid (HA), and sodium alginate (SA) were evaluated in the presence of sodium chloride with an initial influent dissolved organic carbon (DOC) concentration of 5.0 mg C L−1 at different pH levels to establish the optimal doses for in situ Fe(VI) generation. The concentration of Fe(VI) was determined by the 2,2-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) ultraviolet–visible spectrophotometry method. In the case of HA, 72% DOC removal was recorded when applied with 1.5 mg L−1 of Fe(III) and 1.5 mg L−1 of NaOCl (in situ Fe(VI) concentration of 1.46 mg L−1) while 42% DOC removal was observed for SA. Subsequently, the removal of AOM extracted from two bloom-forming algal species, Chaetoceros affinis (CA) and Hymenomonas (Hym), cultivated in seawater from the Red Sea, were tested with in situ generated Fe(VI) at the established optimum condition. In situ Fe(VI) recorded superior performance in removing AOM extracted from CA and Hym, showing 83% and 92% DOC removal when the influent DOC concentrations were 2.48 and 2.63 mg L−1, respectively. A detailed AOM characterization was conducted using liquid chromatography–organic carbon detection.