I presume that you are ...

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I presume that you are meaning that the pre-treatment filters are blocking prematurely rather than the membranes becoming fouled. If that is the case it sounds like the raw water quality is rather worse than the system was designed for and that could be due to a lot of reasons such as others have mentioned silt, iron, biofouling etc.

What you need to do is to identify this and then put in additional treatment steps such as self washing filters and/or chemical treatment to reduce the load going onto the protection filters.