If the bio filter is getting plugged up, either the pre-filter isn't doing it's job or the bio filter is way too small. It sounds like the pre filter needs to be bigger. I'd be cleaning the pre-filter as often as needed so it didn't slow down the water flow and think about building or getting a much larger one, plus getting (or building) a larger bio filter. I've seen pre-filters for 300 gallon RAS tanks that were made from 55 gallon barrels and they still needed cleaning every month.

If the filters are working properly, you shouldn't need to be doing 100% water changes.

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3/4 to 1 1/4 ac pond LMB, SMB, PS, BG, RES, CC, YP, Bardello BG, (RBT & Blue Tilapia - seasonal).