Brown spots on aquarium plants can be caused by algae, high level of nitrates or something toxic in the water. Algae also clings to the glass. High level of nitrates is also indicated by yellow leaves. Over time, brown spots due to high nitrates turn into holes that go straight through the leaf. Brown spots may also indicate that your aquarium plants are being poisoned by chlorine in the water, over-fertilization or something toxic to plants in the fish food.
A regular water change helps reduce the amount of nitrates in the water and also prevents algae from getting a foothold; that water change can help eliminate common causes of brown spots on aquarium leaves. Aquarium Fish.net suggests removing about 20 percent of the water from the tank twice a week. Replace the water with clean tap water. If you have a large tank, you do not need to condition the water; but if you have a small fish bowl, refill it with bottled water.
Substances in the water that are toxic to plants can also cause brown spots on aquarium plants. Check the label on the fertilizer to ensure you are using it properly. Condition your water to reduce the amount of chlorine. Medication for fish may also cause the plant to die. Move a sick fish to a hospital tank if it is almost healed and will not be stressed by the move. You also can remove the plant from the aquarium until the treatment is over and the water has been changed several times.
Reach into the aquarium and pinch off any leaves that are severely spotted. While this will not take care of the problem, it makes your plants look more attractive as you figure out a solution. If a plant is very spotted with brown, remove it from the tank entirely and throw it away.