I'm going to assume that you are employing the SODIS method of water sterilization.
To sum up the details of the process, this method is where you fill plastic pop bottles, (PET), up with rather clear water 3/4 full, shake them up, and let them sit in the bright sun for 5+ hours.
The mechanism this works by is by utilizing the UV radiation in sunlight. The UV itself blasts the microorganisms in the water. The shaking up dissolves oxygen into the water, which then produces ozone, hydrogen perioxide, and other free radicals from the UV light. These dissolved ozone is especially nasty to microorganisms, but they break down quickly and our bodies are not bothered by the amounts remaining.
This method of water sterilization depends on the correct bottle composition, sufficient sunlight, and clear water. If the water is turbid and has a lot of particulate matter, it will prevent the UV radiation from doing its magic.
As far as the still water being a breeding ground for microorganisms, you'd have to leave the bottles sealed for quite some time to have any effect, not the 6-2day timeframe this sterilization procedure requires.
Lastly, microorganisms can grow and multiply in rapidly moving water just as quickly as in a still pond. The reason sourcing water in the backcountry from streams is recommended is because typically, the raging river water has been delivered to the river via rain more recently, than a lake where the water could have been in the lake for years. The motion of the water makes little to no difference. A river flowing out of a lake through a field of horse farms will be a Giardia breeding ground regardless its speed and sourcing that would be far riskier than from a mirror calm lake in the remote mountain wilderness slowly fed by glaciers.