The fern has more spots and looks worse than what the picture shows. Any help would be appreciated.
I see a couple of things in your photo:
The rhizome of you java fern is in the substrate which can lead to rot. The rhizome should be attached to hardscape like stones, driftwood, or even ornaments. You can use thread, rubber bands, or superglue gel to hold the rhizome in place.
What are you fertilizing with? Typically the brown spots/holes shown in java fern leaves of your photo is a sign of a nutrient deficiency; probably potassium. If you are not currently doing so, start using a good balanced fertilizer.