There are many cases where energy can be harnessed in daily activities, the biggest issue is the efficiency and cost of doing so. Most plumbing use wouldn't add up to nearly enough energy to offset the construction.
For example, US average yearly rainfall of 76cm, on a 10m*15m roof, at height of two stories at 5 meters, would give you 1.5kWh of energy per year. That's enough to run the appliances in your home for an hour.
You might be in a more rainy location, or have a larger home, but the end result is still insignificantly small.
my second reaction: on tall building there might be enough height difference to actually bother thinking about it.
So water from showers and sinks, not from toilets. The only contaminant should be a small amount of soap and maybe a few hairs.