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.
Roy 75 Gallon, 2X55W AH Supply CF 8800K, 1XMarineland Doublebright, 2X Marineland 350 Magnum; 45 Gallon Tall, 96Watt AH Supply CF 6700K; 30 Gallon Long; Fluval F&P 2.0 36"/46W; 20 Gallon, 1X26W AH Supply LED kit; all with Press. CO2; (Calcined) Montmorillonite Clay Greater Seattle Aquarium Society (GSAS)