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I have duckweed in most of my tanks, and sponges over the intakes of filters and some power heads.
When the water level is low the water returning from the filter (HOB, spray bar or other) will drive the duckweed under water, and it sure will get sucked up against the sponges of any sort of pump (power head or filter).
I find this to be a temporary problem, though. When the water level is higher the filter return sheets across the top of the water, and pushes the duckweed away from that area of the tank without driving it under water.

Yes, sponges over the intakes of filters and power heads will accumulate debris and will need cleaning. Every few days seems like a lot of cleaning, though. Mine usually go a couple of weeks before slowing down, and another week before it gets to the point that I am worried about the flow. You could try a coarser sponge, for example there are sponges sold for sumps or ponds that are coarser than the Aquaclear sponges. I use a lot of Aquaclear sponges, but if the sponges in a particular tank seem to need cleaning too often I will switch to the coarser sponges. Coarser sponges let the finer debris through for the real filter to trap. I have found that if I use the Aquaclear sponges over an Aquaclear filter the sponge inside the filter (same cell size as the sponge over the intake) no longer does its job. The sponge over the intake is trapping the same debris that the actual filter sponge would have.

Sponges with a larger surface area are a good idea, too. There are 2 main ways to do this. One is to use a Mattenfilter sort of set up. There is a long thread in the Low Tech forum about this. The other is to make a manifold out of PVC with several Ts, and put a sponge over each T. That is the way I do it. Instead of one sponge, and moving 100-300 gph though it, I have 3-5 sponges per filter and each sponge draws less than 100 gph. This also makes the force of the water less at each sponge, so even weaker fish can swim near the sponge or graze on it and be able to get away.

Removing all the duckweed just takes patience. Net out all you can daily and set up a power head that makes a distinct current at the top of the tank. This will push the remaining duckweed to one end of the tank. Remove equipment from that area and keep on scooping out the duckweed. It will take time, but a clear area to scoop it from will really help. By removing it slowly, over a couple of weeks, you are encouraging other resources to take over the nitrogen removal. You could also get some more plants such as Anacharis or Water Wisteria that are noted nitrogen sinks, and easier to handle than duckweed.
 
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