Nile monitors (and water monitors - salvators) do have aquatic adapted behaviors and characteristics. However, there is a big difference between using the water and living in the water.
A nile monitor will do better in an enclosure that is all land with a water container on top of the substrate. I suspect this enclosure you mention is an aquarium. Providing a mostly aquatic enclosure with a rock on which to bask is likely to dramatically reduce the lifespan of your nile monitor into terms of months (or less).
A better setup would be to fill the aquarium with dirt, cypress mulch, or both. Put some hide areas in the enclosure. Get a rubbermaid shoebox container, put it in the enclosure, and fill that with water. Your nile will be much happier in that enclosure. If you really want to see him swim around for a while, toss him in the bathtub (taking care not to drown him, boil him, freeze him, or letting him escape).
Keep in mind as well that your nile is likely to outgrow that aquarium very quickly if properly kept.
The same guide can be used for any size enclosure, in case you are not using an aquarium.
To develop an enclosure with a sizeable water area, you will need a very large cage. Otherwise, just stick with providing water in a container of some sort.
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^x^ Bloodbat ^x^
Monitors, monitors everywhere
and all the food they ate.
Monitors, monitors everywhere,
their parents loved to mate.