So this is my first TES game so I am a little unfamiliar with some of the basics. I left River Wood after doing a couple quests and headed toward that town nearby to the northeast. Upon getting close to the city gates I was assaulted with arrows by the numerous guards. What's going on? I killed the 3 imperial guards transporting a prisoner along the way so I'm thinking that might have caused it. But I'm at a loss for what to do now. I don't have quests anywhere else if these 2 towns are now unfriendly to me. What do I do?

Yes, not sure how high your bounty is but you can try with having your weapons out when they start shooting you, then holstering them and HOPEFULLY they will think that's enough and take you to jail/you pay a fine. Or reload to before you did that. (If your planning on killing any faction members it's usually best to do it while stealthed)

Thanks for the info. Any other ideas out there?