How do you clean wastewater?

This depends on the contents of the waste water but generally this is done naturally be settling and bacteria. There are various methods such as anaerobic, aerobic, activated sludge process, biological nutrient removal and so one. The most basic of which and most smaller towns use are ponds/lagoons.

Medium sized towns use items like trickling filters, digesters and so on. Larger plants use similar items with often the addition of aeration basins. Now with the EPA taking a closer look at nitrogen and phosphorus Biological Nutrient Removal (BNR) treatment plants are becoming more and more popular.

A full description of these processes would be outside of the scope of this forum however, searching any of those terms would provide a wealth of information.