My java fern has black spots

[seangee]

Algae

 

[Byron]

Ok so if it's not a lighting, nutrient or placement issue then what could it be?

I do not think any of this has been ruled out. You were adding too much iron (which in excess causes spots on the leaves as it replaces calcium and the leaves slowly die), the light may be too intense and this would not only affect the plant growth but also algae.