is it turning brown and mushy? or turning brown, but holding its shape?
speaking from my experience, mature java ferns that turn brown but maintain their leaf shape are normal, and eventually new java fern plantlets will grow on the dying leaf
but when they turn brown and just rot to mush, then there is a problem . . . could be your water, could be your light, lack of nutrients, etc.
do you have them planted in the substrate, attached to something, or free-floating?