Waste water flow rate in small municipal wastewater treatment packages.

In small wastewater treatment packages working through extended aeration process, inlet water flow rate is more than average produced wastewater due to limited flow rate of submersible pumps used to transfer raw waste water to the package and pump should start and stop periodically. Since the automation system used in these packages is the least and can not control flow rate properly, What consequences does this issue has? Does semi-intermittent (on-off pattern) working of the package has any adverse effect on the process?