You wanted it, you got it. Now you can modify terrain in your Cities: Skylines city while you play. The Terraform tool mod is still a work in progress, currently in version 0.8, and I found it a bit buggy. Still, it's neat. You can load up your existing city and use a new toolbar to raise and lower the land, paint hills, cliffs, mountains, and valleys.
Once you subscribe to the mod, you'll find a new icon on your dashboard, next to your budget and policies icons. Clicking it brings up a panel of terraforming options, allowing you to right or left click on the ground and raise or lower the sections of the map you've highlighted. Pressing + or - on your keypad increases and decreases the size of your brush. This way you can make small adjustments like hills, or make the brush size massive and start growing mountains.
There's a cost associated with massive earthwork projects, naturally, so either keep a close eye on your bank account, or activate Skylines' unlimited money mod before you start. And, before you start mucking around, you might want to create a new save of your city. Somehow I accidentally created a massive gorge, and couldn't re-raise the land. Again, there are some bugs.
The strength of the tools can be adjusted as well, by holding Shift and using the + and - keys again, which should help give you more control over your terraforming. You can't raise or lower land if something is currently built on it, including roads, so if you imagined having skyscrapers on top of a mountain, you'll have to build the mountain first.
Water, naturally, responds to land placed in its way, or, I imagine, removed from its path, so hey, you might have a new tool to create a horrible disaster for your poor citizens.