Definition
A primary filter is the vessel-mounted first-stage fuel filter, usually incorporating a water separator and a clear bowl, that removes water and coarse contamination from fuel before it reaches the engine-mounted filter.
The primary filter does the heavy work. It catches water and the coarse contamination that a boat's tank inevitably produces, protecting the finer engine filter and the injection system behind it.
The bowl is a diagnostic instrument
What collects in the clear bowl tells you the state of your tank without opening it: water sitting below the fuel, dark slime from microbial growth, rust scale, or sediment. Draining it on a schedule and noting what came out turns a repeat filter blockage into a diagnosis. See how to tell if you have diesel bug.
Sizing and micron rating
Primary filters come in flow ratings and micron ratings, and the primary is deliberately coarser than the secondary. Fitting a fine element in the primary position blocks it quickly without improving protection. Match both to your engine's requirement.
Where you meet it
On every serviceable installation, in every filter change, and as the first thing to check when an engine starts then stops.