Nah it's cool, that just means channeling the river it is. The simplest way to do that is to dig a tunnel right up to (but not breaching) the wall of the river, underground. Install floodgates (make sure the installers are on the safe side and not towards the river) in the tunnel. Then you can link the floodgates to a lever, test the connection, and channel out the wall of the river from above. Now you can plan wherever you want a cistern, connect cistern to tunnel, lower floodgates, and you have an endless water source. Constructing fortifications will allow water and vermin to pass, but is supposed to filter out carp and things. May or may not work. Don't forget to depressurize before you let the cistern feed out somewhere, or watersports may ensue.
The cavern feed I mentioned is:
Step 1
Dig out room adjacent to surface of the water.
~W...
~W...
~W...
~=empty space, water's surface on Z-1
W = natural stone wall
. = floor
Step 2
Channel out the wall tile, and 1 tile of the room.
~W...
~HH..
~W...
H = channeled tile
Step 3
Construct a wall to plug the gap, build floor bars ( alt + b I think) over the feed in the floor.
~W...
~Cb..
~W...
C = Constructed wall
b = floor bars
A screw pump can now pull water up through the bars and feed an aqueduct into anything else you need on that level or lower. I've had 5 building destroyer beasts swimming around a grate like this for multiple years, they don't seem to be able to get in, as long as they're lower than the bars, and the channeling/built wall forces that. You can operate the pump manually whenever cistern needs refilling, just keep in mind that pumps cause pressure too.