Hi Kgabo, treatment options ...

Hi Kgabo, treatment options also depend on what you plan to use the water for.  If you aim is to treat the water as a drinking water supply, you will address the E.coli count with normal disinfection (usually chlorine based chemicals) after flocculation, clarification and filtration (which will also remove a percentage of the e.coli).  The eutrophication status may present other problems if it results in excessive algal growth which may require activated carbon to remove microcystins, tastes and odours.  If the water is to be used for irrigation or recreation purposes, it would be wise to install some disinfection system to prevent excessive biofilm growth in the pipelines and irrigation sprayers/droppers and to protect workers/users.  

Although the long term approach of the writers below of addressing point sources is fully relevant and supported, this may not help you in the short term, or it may be very difficult to achieve (e.g. sewage discharge from a town or city).