Nobody knows with absolute certainty all of the ways a magnetic field can affect a moving fluid. There are several theories, however one seems to be the most logical and widely accepted.
When a fluid (fuel, water) is passed through a properly aligned magnetic field, changes occur in the fluid on a molecular level. In fuel, the random molecular bonding of impurities is prevented. The dispersion of these molecules, sometimes referred to as “magnetic homogenization,” allows the fuel to burn more completely. The result: better fuel efficiency and lower emissions.