Depending on your location and specifics of your application, I would consider ozone. Besides its microbial and algacide properties, it can also reduce fouling on the heat exchange surfaces, and tends to moderate pH towards a neutral value of ~7.4. It should be used with side stream filtration...
You did not specify if you want a continuous pumping operation (as in a water supply well), in-situ (as in strict remediation), or a pump and treat (extraction just for treatment, then discharge to a municipal storm sewer). I assume that you want a water supply, and that supply must be treated...
