This may not be the most tactful time to bring it up, with much of Pakistan underwater and many millions homeless, but Pakistan's real problem is not too much water. It is too little water — and one day it could cause a war.
The current disastrous floods (to which the response of both the Pakistan government and the international community has been far too slow) are due to this year's monsoon being much stronger than usual. But that is just bad weather, in the end: Every 50 or 100 years you can expect the weather to do something really extreme. It comes in various forms — blizzards, floods, hurricanes — but it happens everywhere.
The long-term threat to Pakistan's well-being is that the country is gradually drying out. The Indus River system is the main year-round source of water for both Pakistan and northwestern India, but the glaciers up on the Tibetan plateau that feed the system's various tributaries are melting.