Harmful algal blooms (HAB) release microtoxins that contaminate drinking water supplies and risk the health of millions annually. Crystalline ferrate(VI) is a powerful oxidant capable of removing algal microtoxins. We investigate in-situ electrochemically produced ferrate from common carbon steel as an on-demand alternative to crystalline ferrate for the removal of microcystin-LR (MC-LR) and compare the removal efficacy for both electrochemical (EC) and chemical dosing methodologies. We report that a very low dose of EC-ferrate in deionized water (0.5 mg FeO42− L−1) oxidizes MC-LR (MC-LR0 = 10 μg L−1) to below the guideline limit (1.0 μg L−1) within 10 minutes' contact time. With bicarbonate or natural organic matter (NOM), doses of 2.0–5.0 mg FeO42− L−1 are required, with lower efficacy of EC-ferrate than crystalline ferrate due to loss of EC-ferrate by water oxidation. To evaluate the EC-ferrate process to concurrently oxidize micropollutants, coagulate NOM, and disinfect drinking water, we spiked NOM-containing real water with MC-LR and Escherichia coli, finding that EC-ferrate is effective at 10.0 mg FeO42− L−1 under normal operation or 2.0 mg FeO42− L−1 if the test water has initial pH optimized. We suggest in-situ EC-ferrate may be appropriate for sporadic HAB events in small water systems as a primary or back-up technology.