If you enable Vsync the problem is likely to go away. Vsync will cap your frame rate at 60 FPS. Skyrim seems to have issues when the FPS goes higher than 60.
To enable Vsync browse to the location on your computer where your Skyrim save game files are such as:
C:\Users\[Your Username here]\Documents\My Games\Skyrim
Make a backup copy of skyrim.ini and put it somewhere you will remember.
Open the file skyrim.ini. using any text editor and In the 'Display' section, look for a line that reads:
iPresentInterval=1
When the value of this variable is 1 then Vsync is enabled. When it is 0 it is disabled. If you don't see this line in Skyrim.ini then add it to the end of the 'Display' section of the Skyrim.ini file. Save the the skyrim.ini file and run Skyrim.
Pros When Vsync Enabled:
- No more water flicker
- Less objects flying around at the speed of light when you walk near them or open doors and whatnot
- No weird clanking sounds (usually heard in small interior cells) like objects being knocked around when they aren't
Cons When Vsync Enabled
- For me, I have a bit of cursor lag when navigating menus. It's not real bad, but noticable.
Hope this helps.