I found this on Google:
Why do some cats put their toys in their water or food dish?
Cats look upon their food area as part of their territory, and that particular area of their territory usually doesn't change from day to day - so the cats are likely putting their favorite toys away in a "safe" place. Some cats will consistently put away their toys when they're through playing with them - you might try putting your cat's toys in a small basket near one of his favorite spots and see if he will put them away on his own.
Believe it or not, this is a very common practice among both cats and dogs. It just might be that your cat is trying to find a "safe" place for her favorite things. It often happens that the toy that ends up in the water or food bowl is often a toy that has recently been enjoyed by your cat, or even by your cat with you. In the wild, cats often take their prey back to their "nest" area, and hide it from predators. Indoor cats don't really have a "nest" per se, so they often consider their food and water dishes and that area in general as the "safest" areas within their "territory".