The details of the plant do not show up very well in the pictures you have taken. However, this does not look like a deficiency. It looks like spot algae and black beard algae (BBA). Also, java ferns in general do not make good indicator plants of deficiencies. They tend to naturally grow tattered looking leaves.
You can use hydrogen peroxide for the spot algae (it will take several spot treatments) and flourish excel for the BBA (only 1 or two treatments per patch of BBA). Use a syringe to suck up either liquid and slowly squirt it onto the algae underwater to kill it. The spot algae will bubble vigorously when you treat it and the BBA will turn red the next day, then gray a few days later, then decay away over the next few days/weeks.
You can use hydrogen peroxide for the spot algae (it will take several spot treatments) and flourish excel for the BBA (only 1 or two treatments per patch of BBA). Use a syringe to suck up either liquid and slowly squirt it onto the algae underwater to kill it. The spot algae will bubble vigorously when you treat it and the BBA will turn red the next day, then gray a few days later, then decay away over the next few days/weeks.
