Lack of good urban planning. Houses are built before everything(water, sanitary facilities, water drains). And then everything is planned around them. What you get is semi-ghetto areas, where everything has to be crammed in without any intelligent design. So you get small sewage pipes which don't have the bandwidth to carry waste water, let alone any reasonable sewage(like toilet paper).
Now imagine entire mini cities rising up like this. How do go around building sewage drains? They too come up randomly, emptying into lakes, ponds, former rivers.
This is exactly the case near my home in Bangalore. 10 years after the houses were built municipal corporations are now putting in an after thought. In fact roads are so badly planned that there people who have encroached the entire section of the street discontinuing the road from one corner to the other. They get away by bribing local corporators.
Also there is no door-to-door garbage collection facilities so people discard household waste onto some corner in every street which has to be later cleaned by garbage men who show up once in 2-3 weeks, hence mosquitoes and dengue like diseases.