If you would have waited, you could have installed a screw pump (B - M - first option, requires 1 block, a screw trap component and a pipe) in first, which would have pressurized the water down a directed path and been a 100% clean to drink (with only the slightest amount of mud, which can be fixed by making the ditch 2 z level deep)
Example.
Z level 1 - Water (W) comes in from the river/whereever into the extraction point (X) (~ stands for water and is more important for the second example, here it shows a 2 deep ditch that reaches to Z level 1, the water here should be lightly muddy, while the water above is clean, filling from the bottom to the top)
WWWX ~~~~~~~
Z level 2 - Water is then drawn via the grate above the extraction point (G) and the screwpump that draws from the tile beneath and behind in the desired directions N/S/E/W , after being hooked up to gears to activate the screwpump, or manually pumped by dwarves (easier setup, but requires access and allowances for dwarves to take eating/sleeping breaks) will pick it up and push it out to that level, the water should travel down the path you set up for it with good pace due to pressure.
G(SP) ~~~~~~~
Z level 3 - This is the z level your dining room is currently standing on with your dwarves looking down into your channel, the screw pump stops the water getting this high. As already suggested by other people on the thread, you might want to cover it up with something or install something nice over it. Grates allow dwarves to drink and clean themselves through it,
but are destroyable from the top, not the bottom (grates can also be decorated to be fancy, experiment with stuff like glass i recommend, just as long as you dont mind things being broken)
I hope this simple diagram helps.