There isn't really a safe way in the game to dig into the bottom of a river. This is because there isn't really a safe way to do this in real life, either.
If you insist on doing it this way (and you've already dug out the level below the river, which I assume you have), you can build build an C-up-stairs on the tile below where you want to put a hole in the ceiling, which will give a dwarf access to the tile above, where you can dig a down-stairs. (If you haven't dug out the level below the river yet, you can just dig an up-stairs instead of constructing one.)
But seriously, I don't recommend doing this. A much safer way to do it is to dig out your entire water system dry, with a 1-tile dam on the surface between the river and the intended water inlet. Build all your floodgates and hook them up to switches and everything you want. Be prepared for a dwarf to build a floodgate from the wrong side and wall themself in; they always do.
Then, when everything is dug out and built, and you're very sure there are no dwarfs having a party in the sewers, dig a channel in the one tile on the surface separating the water system from the water. The channel designation means the dwarf should stand above and dig a hole without stepping in it, which is the important part. Make sure you designate the channel on the level above where the water is (outside, probably), because it actually removes the wall from the level below. If you did it right, water will flood in as intended. If you did it wrong, shame and mortification. I recommend putting an initial floodgate right behind the dam, so that you can shut everything off at once if there's a problem.