Is it possible to build a new river across a land barrier?

I'm trying to make something like the Panama Canal - there's a piece of land, less than a hundred blocks wide, that if completely removed, would connect two larger oceans. So I did the obvious, crafted up a dozen shovels, and started clearing. The first problem - three tiny lakes in the region, which, when I dug up to them, started water flowing in all directions, making movement to continue digging downward, very hard. The second problem - opposing water currents due to the water generators from the lakes, which my boat can't get through (could also be a problem with the water not being deep enough, not sure).

I don't understand the water mechanics well :) So I'm wondering if it's even possible to build, what is basically a new river crossing a land barrier, with sufficient depth and smoothness of water, that one of those rickety wooden boats can survive crossing.

And if so, how? Is my current situation salvageable, or would I have needed to treat the lakes differently?

Just for the record, I'm not asking how to make an aboveground canal using wood + water sources, I have read about those.

Update - the rapids I first created, were salvageable, but required filling the entire area with blocks to drain it. Fortunately, (unlike the original Panama Canal) no workers died of malaria - although many annoying pigs/cows got the axe.

And had I known how long it was going to take, including boating to/from the site every day/night cycle - I'd have walled/roofed the whole thing over, so I could work there at night. I suspect it would have been faster overall...

What you should do is make the water only one block deep, so that it all levels out. See the question that ZoogieZork posted. After that, you can dig as deep as you want and the currents shouldn't appear.

In general, here is a good technique for building rivers (top-down view):

█▒█▒█▒█▒█▒█▒█▒█... | █ = block
.█▒█▒█▒█▒█▒█▒█▒█.. | ▒ = water source
..█▒█▒█▒█▒█▒█▒█▒█. | . = empty block

First, you want to dig out a path for your river. Place alternating blocks and water sources along where your river is dug out so it looks like a checkerboard. Then, destroy all the blocks. Because there are water sources every other block, the space created by the blocks being destroyed will turn into source blocks themselves and create a nice and smooth river.

In your case, you would probably be able to build this pattern right up to one block before the lake. When you've destroyed all the blocks and the river is nice and smooth, you should be able to connect the lake and the river and the connection between them should level out.