A fuel filter removes solid particles (rust, dirt, paint flakes, biomass) from diesel fuel by trapping them in a media element. A fuel/water separator does the same particle-trapping work AND uses a coalescing layer to drop free water out of the fuel into a sediment bowl, where the driver drains it manually at fuel stops. On heavy-duty diesel trucks, most engines run both: a separator as the primary first-stage filter and a fine spin-on as the secondary. The separator catches what fuel-station storage tanks shed; the secondary catches anything fine enough to slip past the separator before fuel reaches the high-pressure injection pump and injectors.
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