What waste water do you mean? Do you mean treated sewage? This makes sense if there is a lot of sewage being released into the sea. To the best of my knowledge, the excess salt is in water that has had a percentage of the water removed. The higher salt content water is then dumped back into the sea. It would certainly seem easy to just have treated sewage and the high-salt water from the plant poured out together from the same pipe. For all I know, they already do this.

However, there will tend to be less fresh sewage water than high-salt water. After all, the fresh sewer water originally came from the desalination plant, but not all of the fresh water will return as sewage. Unless they get a fair amount of rain, but countries that rely on desalination often have little rain.