Google regards
www.your-site.com & your-site.com as 2 seperate web sites, therefore, if there are links to both URLs your site will suffer Google's duplicate content penalty & drop in their rankings.
If you are registered with Google Webmaster Tools (GWT) go to the 'Tools' tab & use the 'Set preferred domain' to set either the www or the non-www version of your site.
Ideally you would also want to have a 301 redirect (permenantly moved) from one to the other. You can see how to do that using the .htaccess file as described in the previous post.