High disk watermark exceeded even when there is not much data in my index

From Index Shard Allocation:

… watermark.high controls the high watermark. It defaults to 90%, meaning ES will attempt to relocate shards to another node if the node disk usage rises above 90%.

The size of your actual index doesn’t matter; it’s the free space left on the device which matters.

If the defaults are not appropriate for you, you’ve to change them.