Can you provide a bit more information? What size sewer line will you be measuring from? Is this a temporary measurement or do you need continuous flow measurement?
The best way is using a non-intrusive technology such as a mag meter or a doppler meter. If you have a sewage lift station, you can also use volumetric measurement by electronically monitoring the on/off cycles of the pumps. The time between pump off and pump on, knowing the volume pumped (cross sectional area and float elevation difference) will give you the flow rate for that period. There is a commercial product offered which uses this principle (I believe it is called a "Volumeter", and I believe Flyte pumps can also provide a similar system. Alternatively, it is easy to do using any inexpensive SCADA unit.