I have noticed that it does not always work that way.
It seems to me there is a reserve of nitrates in the substrate. When I measure the tank (hold ruler up to side and mark the halfway point, half the height of bottom of substrate to top of water) and remove water down to the 50% mark I am actually removing more than 50% of the water, since some of the volume left in the tank is really substrate. But anyway, pretend that I really removed 50% of the water.
The nitrate is often a little higher than I thought it should be.
If I remove the water by taking it from under the substrate I think I am removing some of the nitrate from the substrate. If I still remove water to the 50% mark I am still removing slightly more than 50% of the water, but I am removing the water that has been in contact with the substrate, so might be a little higher in nitrates. So the final test does show slightly lower nitrate than the other method.
To remove water through the substrate I dig a hole in each corner and push the tubing into that hole. Keep the substrate from going up the siphon, but as much as possible pull the water from the substrate, not the main bulk of water in the tank. Take about 25% of your water change from each corner.
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