Build it like this (side view
~~~
T
T GTT
TTTTTTTT
Where T is the tunnel, G is a floor grate and ~~~ is your happy little stream.
Creatures are completely oblivious to objects above them and cant destroy that grate.
Wow, you want him to flood his fort don't you?
Agent 86: Follow Avo's advice, but look up "flooding" on the dfmagma wiki, you'll want either a "u-bend" or diagonal depressurizer in as others have already said.
Also I recomend making your "fishery" a large room completely covered in floor grates like so:
FFFFFFFFFF
GGGGGGGGGG
GGGGGGGGGG
FFFFFFFFFF
GGGGGGGGGG
GGGGGGGGGG
FFFFFFFFFF
GGGGGGGGGG
GGGGGGGGGG
FFFFFFFFFF
Channel out where the "G" are and dig under 'middle' two the "F" rows, since grates can't support each other you need those actual floors. This gives you a large fishing area (10x10 room, 60 fishable tiles) (you can make it bigger or smaller as you prefer) and you'll encounter less "There is nothing to catch in the [region] swamps" cancelations.
In fact I tend to eventually build 8 fisheries, one in each cardinal and ordinal direction from the fort proper. Then I rotate every few seasons which ones are set for fishing... back in 40d you could overfish a spot and it could become permanently depleted, I'm not sure if that still applies, but I still treat it as though it does.