Magnetotactic bacteria (MTB) combine passive alignment with the Earth magnetic field with a chemotactic response (magneto-chemotaxis) to reach their optimal living depth in chemically stratified environments. Current magneto-aerotaxis models fail to explain the occurrence of MTB far below the oxic-anoxic interface and the coexistence of MTB cells with opposite magnetotactic polarity at depths that are unrelated with the redox gradient. Here we propose a modified model of polar magnetotaxis which explains these observations, as well as the distinct concentration profiles and magnetotactic advantages of two types of MTB inhabiting a freshwater sediment: a group of unidentified cocci (MC), and a giant rod-shaped bacterium (MB) apparently identical to M. bavaricum (MB). This model assumed that magnetotactic polarity is set by a threshold mechanism in counter gradients of oxygen and a second group of repellents, with, in case of MB, includes H+ ions. MTB possessing this type of polar magnetotaxis can shuttle between two limit depths across the redox gradient (redox taxis), as previously postulated for M. bavaricum and other members of the Nitrospirota group. The magnetotaxis of MB and MC is predominantly dipolar whenever the presence of a magnetic field ensures a magnetotactic advantage. In addition, MB can overcome unfavorable magnetic field configurations through a temporal sensing mechanism. The availability of threshold and temporal sensing mechanisms of different substances can generate a rich variety of responses by different types of MTB, enabling them to exploit multiple ecological niches.