It's a bit chaotic, but that's fine. I usually prefer to preplan my whole fort's layout from the beginning so I have fancy designs, catwalks, chasms, and the like, but before you know what you're actually likely to need, not doing such things is fine.
You'll probably find it impossible to actually drain those two murky pools into the stream; there's simply not enough water in them to spread off the maps you've given to the south.
Your next step should probably be a dining room at this point, for added happiness.
Also, you'll get better at this as you get better at the game, but in the future, try making more effective use of z-levels. It's far more efficient to put your stockpiles directly above or below your workshops when possible so your workers have less distance to haul things. It also makes it easier to set exactly what materials your dwarves use most of the time, which is another plus. For maximum efficiency that, generally, means staircases either in the same chamber as the workshops, or directly outside a door from them.
Overall, I think your biggest problems at this point are twofold. First, you're using a tileset and it's making your screenshot a bit difficult to read (

), and second, your design on this z-level isn't very extensible. I suspect that you'll have a bit of trouble once you start getting more dwarves to deal with, as you'll probably need to repurpose all of the rooms here, and perhaps even tear them down entirely and rebuild them elsewhere. Also, it looks like your first bedrooms aren't in rock (I can't tell because of the tileset), so you won't be able to smooth them at all. That makes improving bedroom quality much harder.