In order to correct this problem, you must first determine if an action (manual or automatic) has been taken against your site. Based on reading your question, it seems likely that you may have been penalized due to duplicate content; however, it is imperative to understand if one or more rules have been violated. If indeed you have been penalized, it is possible that the penalty had to do with duplicate content (as stated above). Subsequently, this may have something to do with your search and filter features - as displaying the exact same content on different URL's and doing so without indicating to Google which URL is the preferred version read more about canonicalization here - could also be your problem. According to Google's Webmaster Guidelines for duplicate content:
If your site contains multiple pages with largely identical content,
there are a number of ways you can indicate your preferred URL to
Ok, so what you need to do is diagnose what, if any, problem exists, fix it, and then submit your website for reconsideration.
Here are step-by-step instructions:
Sign in-to your Google Search Console Account. If you don't have one, it's about that time that you create one.
Make sure that you have verified all versions of your website. This is the only way to know that your diagnosis is complete and accurate (not to mention, it's the proper way to use Search Console).
Note: All versions of your website include the "www" version and "non-www" version. If you have an SSL certificate installed on your website, you should also verify the "https-www" version of your site, long with the "https-non-www" version of your site. In the latter situation, one site can have 4 instances in search console.
Visit the manual actions section on all of your sites to see if Google has taken any actions on or against your website.
If Google has taken a manual action, they will actually tell you what you did wrong, or the general Quality or Content guidelines that you are in violation of.
Additionally, review the "Security Issues" in Search Console to make sure that there are not any other problems with your website - definitely check this off the list.
Click on "request a review" to ask Google to reconsider your site.
If you want to hear and see this info from the horse's mouth, I've included a link to a youtube video of Matt Cutts explaining exactly what you should include in a "proper reconsideration request."
Best of luck to you!