Nice sewer tunnels are like :
topview:
XXXXXXXXXX
~XXXXXX+++
~~#~~~~+~~
~XX+++++XX
XXXXXXXXXX
sideview:
X X
XX~X
x=wall ~=water +=floor
With mainenance access/escape pathway including a bridge and a grate.
I don't usually bother with drainage mechanisms, but a floodgate linked and some pumps linked to work should suffice.
The wellshafts/exists/access wells are naturately incomplete without a winding staircase (using ramps).
Nicer tunnels can be dug offcourse, but take a lot of room.
I still plan to create a multilevel dungeon with leveroperated grates, hatches and floodgates. One level fresh water access, the level below: waste disposal.
Also a Windaria type fortress appeals to me greatly.
It seems that stagnant water generates miasma: I have a small fort wich had no flowing source of water, so I cut some corners and used buckets to fill the ruidimentary well shaft from the evaporating ponds outside. (normally, the dwarven way is to redivert the pools to a smoothed underground cistern.
ehm. I had exceptional periods of miasma exploding out of the wellshaft into the fortressproper, without any visible source. (there were plenty of eruptions from the buthchers' and the catlover's chambers, but these could be accounted for by rotten items.)
The water never became murky though, even when I started to use it as a dumping place for the other smelly stuff.
Oh, ahem, the point was: you also need buckets to give water to sick dwarves, the INTERRUPT message states this, but you never know, you could have ignored it.
Dwarves cannot get at water below a level of 4, also when wading through partially filled water tiles (or ramps!) they panic because of dangerous terrain.