Isn't my filter supposed to keep my fuel system clean?

Well, filtration simply cannot and will not do that. At best, filters, separators and centrifuges remove debris suspended in the fuel before the fuel reaches the engine. Stopping, preventing or reversing the process of fuel breakdown is a completely different matter that can be addressed and resolved with ALGAE-X® Fuel Conditioners. It is not very likely that filtration, (either the filter on the engine, or an external filtration system) will remove the sludge coating from the walls and baffles of your storage tank and the use of biocides will almost always aggravate the situation. Filtration has no effect on
fuel break down processes whatsoever.

Filters are primarily designed to remove in-organic debris from the fluid stream and, as we have seen, they become clogged with organic debris, resulting from fuel degradation. The water separator is designed to remove free-water. However, a separator, filter combination or centrifuge cannot remove emulsified water. Free water in fuel can simply be removed from the fuel stream with the use of a water separator. Several well-known and very efficient combination Filter/Water separator devices are on the market. They are essential in any diesel engine application.

Simple in-organic debris, dust, sand, rust, etc. can easily be removed from the fuel stream with a filter. That is what the filter was made for. This in-organic material will be trapped in the filter without clogging it. Most of the debris we see on the filter elements (the stuff that plugs our filters) is the result of the fuel having begun to form solids.