Suggestion: introduce new liquid - dirty water, and change the way water interacts with other liquids.
Two basic rules:
1. X clean/dirty water + Y other liquid = X+Y dirty water, for as long as X > Y.
2. When amount of clean/dirty water in pipes, containers, wagons or buildings is < 1 it evaporates, leaving them clean.
This will allow the player to "flush" his liquid networks and wagons with water, making them available for other uses.
Additionally, the game will need a way to get rid of dirty water:
3. Dirty water can be dumped, creating considerable amount of pollution.
4. A new building: water purifier. Consumes small amounts of coal and converts dirty water to clean water, producing some pollution as side effect.
For bonus points, water purifier building should cost lots of Uranium and have a Jefferson statue inside.