Water is added in the terrain tab, you can add water per-tile - note that it adds a water layer encompassing an entire tile. You can adjust the height of it by putting your terrain brush tool thing onto 'water' mode and setting the radius to 300. Note, you can only change the height of the water at each corner of the tile.
With traffic light timing, you need to get the Inofficial SDK, and familiarize yourself with OmsiObjEditP.exe.
The others are just normally spline creations.