Is the water also allowed to flow through the substrate? If you set it up with the intent of the water in the feature remain just in the feature, perhaps there is a leak somewhere allowing the water to pass into the land area?

If you closed off the top of the terr, that would reduce evaporation but would also negatively impact your air circulation. Along as the land portion is not an unintended "swamp" as a result of undesired water leakage, I'd probably just plan on adding more water when needed.

Any photos?

I didn't really want it to leach into my substrate and so i have it sealed off. It is sealed and I keep checking to see if my substrate is flooding at all, it doesn't seem like it is. So I'm just going to keep monitoring it and adding more water when needed. I will try to upload a couple pics when I get home