You actually can "loose" water. Of course it doesn't disappear, but if you divert water from a river to your field, the river will have less water. This gets even worse, if you use low-tech methods to irrigate your field. Most farmers in sub-saharan Africa use plain flooding to irrigate their field, which is very wasteful (most of the water just evaporates).
Fresh water that is stored in rivers and lakes is great for drinking, irrigation, transportation, and food production. Once it hits the salt of the sea, though, it takes huge amounts of energy to de-salinize it to make it drinkable again. So if the rains stop falling or the spring run-off from the mountains never comes, and you don't live on the coast, where do you get your water?
Apart from global warming we need to manage our water resources better. There are projects in the region that have diverted water for other uses when it should be going to maintain water levels in the lake.