Jasco puts out a water-based product called Cure-Seal. Although it doesn't have toxic warnings on the label, you should still let it cure for a week or so, then make several water changes after you refill your waterway. I have inadvertently splashed it onto some moss with no obvious ill effects, so I think it's safe, although I don't know for certain. The smallest amount I could find at Home Depot was 1 gallon.
I have found another leakage problem that occurs using Winterstone that I imagine might also happen with cement or anything with a porous or rough texture. The water will tend to wick up and over the edges due to a kind of capillary action. I've had to go back and put extra coats of sealer on the top edges of the container.
There may be even better sealers available from pond and swimming pool supply houses, as these are usually built with cement. As Homer pointed out, cement is extremely alkaline. Sometimes cement or mortar is treated with muriatic acid to neutralize it, but this is strong hydrochloric acid and very corrosive. You might try removing the water, filling the container with white vinegar, then allowing it soak for awhile before drying and sealing it.
My son is a geologist and stone sculptor, so may have a better solution for this problem. I will ask him and let you know.
-----
Patty
Lost River, Idaho