Basically imagine this as a medieval version of the electric power grid. The energy from the water can be quantified by the amount of stamina it takes to obtain water by hand.
1) Aqueducts to move water to mills and cisterns-medieval power lines.
a) wooden aqueduct- low volume of water per second
b) stone aqueduct- medium volume of water per second
c) castle aqueduct- high volume of water per second
2) Windmills and animal powered norias that supply water-medieval generators
a) advanced water well- windmill on a water well that supplies water
b) noria- animal powered water pump that supplies water faster than a windmill, but uses a draft animal that you have to feed
3) Water wheel that uses water transmitted by aqueducts as a source of power. the water wheel will have modules on it that you can build specialized implements into it
a) Sawmill
b) Flux mill - after you guys develope a better way of making flux, you put charcoal in the mill and it makes flux. But you have to have level 90 in alchemy to do it
c) hammer mill - makes tools faster without a blacksmith's hammer
d) blast furnace - a bloomery with a bellows that is powered by the water wheel and doesnt use up your stamina
e) kiln mill- a faster way of making charcoal and glass, but also enabling auto crafting. Bellows is powered by a water wheel
f) stone shaping mill- shapes stone, granite, and marble at a faster rate and you lose no stamina
g) tanning mill- tans more leather than a tanning tub at one time, but takes just as long to do it
4) Cistern- a container that stores water like a chest does
a) You won't have to expend time and energy to obtain water pouches.
b) the cistern will be refilled automatically by the windwaterwells and norias or other cisterns using aqueducts
c) 3 levels/sizes-wooden, stone, castle

*for example 1 water=10 stamina, for a stone shaping mill it takes 30 stamina to make 1 shaped rock. So for the water wheel to perform this action it will consume 3 water pouches to allow the stone shaping mill to make 1 shaped rock*