you may need to consider scour and for several reasons
1. Long Term Degradation - is the stream bed profile agrading or degrading - that is, is the stream bed in equilibrium, or not? Is there headcutting occuring downstream of the sewer crossing which may move upstream?
2. Local Scour - as described above by raweber, this could be caused by a flow contraction such as that caused by a bridge, culvert, etc.
3. Bend scour - caused where the channel has significant curves which cause transverse currents and waves
4. Low flow incisement - Is the depth and location of the low flow channel fixed, or will it vary over time?
5. Is the channel stable under 100 year flow rates? Under very high flow rates, will flow become supercritical? Will sediment transport rates increase greatly to cause degradation of the channel?
As a defense against a sewage spill, I would also recommend that the sewerline be constructed either within a steel casing, or use iron pipe with mechanical joints. You may also consider encasement in concrete.