Surface sediments at the former military base Hradcany, Czech Republic, heavily contaminated with hydrocarbons, were remediated over years by air-sparging. The sediments show a strong magnetic enhancement at the groundwater fluctuation zone. Here we describe the isolation of a new Fe(III)-reducing and magnetite-producing bacterial strain Geothrix fermentans HradG1from this magnetic and redox-dynamic layer. This isolation underlines that the genus Geothrix is a relevant group of bacteria in hydrocarbon-contaminated environments that undergo dynamic oxic-anoxic redox fluctuations. The Fe(III)-reducing metabolic activity of these organisms potentially leads to changing magnetic soil properties that can potentially be used to identify biogeochemical hotspots.