I would think that if your substrate is large enough to allow large particles to pass through it, then the undergravel idea might work ok if the water is then taken outside the tank and cleaned somehow. What ive heard of undergrounds is that the waste is sucked into the substrate and bacteria breaks it down there. This doesnt work well with turtles, but excellent with a light fish load.

I would think and underground filter- with large, loose gravel, which has the uplift tube hooked to somekind of canister or wet/dry filter would be ideal for a turtle tank, therefore sucking waste from the entire floor of the tank, instead of just an uplift tube. I may incorporate this idea into my next DIY filter.
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