This might not actually be a problem, but it doesn't feel intended so I made this issue. Feel free to close if this is intended behavior.

With the default settings for version 0.15.0.0:

Kerbal water per day: 0.241663/day
Kerbal waste water per day: 0.30775/day
Water purifier 1.25m intake waste water: 0.94/day
Water purifier 1.25m output water: 0.74/day 

Kerbal waste water per unit of water: 1.2435
Purifier water per unit of waste water: 0.7872
Net water output per unit of input water: 1.0024

100 units of water -> 124.35 units of waste water -> 100.24 units of water

This is without any bonuses; with bonuses, the net gain increases. With larger purifiers the net gain slightly increases.
To match the desired efficiency multiplier of 10.0, the purifier outputs would have to be changed to:

Purifier 1.25m: 0.66 water per day
Purifier 2.5m: 0.33 water per day
Purifier 3.75m: 0.37 water per day

The problem may persist after bonuses, though.