When the water goes down, invest in getting good advice on how to prevent your basement from getting wet again. When you put your house on the market, you must be honest that your basement took on water. You will need to show that you did something about this to keep it from happening again, or you may not be able to get someone to buy the house...
If you think about the low amount of interest you make on your extra money, and how much you're paying in interest on your mortgage, you may do better to up your monthly payments. Putting some extra money towards the principle each month, or quarterly, will lower what you pay in the long run significantly.
If you put a lump sum down, and then something happens and you need the money, you could really hurt yourself there. That's why monthly or quarterly is probably better.
Talk to a real estate agent about the value of your house and if it makes sense to spend money on an addition.