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Depending on what you use for growing medium, you could cover it or enclose it in landscape cloth. If you ventured into the hydroponics as suggested you could grow in rockwool or similar material, or if you have old abs pipe lying around you can core holes in the side of it to place your plants into it.Hydro or Aerop[onic solution would be fussy and a pita with sun, nutrient, evap algae etc.I've never heard of it, but if as suggested there is special pond dirt,,,,, that sounds the simplest
place the pickup for the pump in a clay/tin plant pot or plastic bucket so that the lip is a few inches below the serface (sometimes with holes around side) and some rocks in it, it can even be laid on side opening faced away from silt source. it is what we use for recirculating water for a gold sluice in a tub to keep 12v pump from clogging!