When I wrote the article on removing unnatural link penalties last month, I didn’t know it was going to morph into a series (hoped is probably the better word), but here we are. From my extensive research, I know there are a ton of webmasters not so silently suffering, and they are replete with questions that seemingly have no answers. The essential question, gnawing a hole through their gut, is:

Google has removed the manual penalty from my website, but the traffic hasn’t returned. Why is this and how long will it take before that sweet Google search traffic returns?

I know this because I’m in the same boat. I have two sites that have had manual penalties removed (July 3 & July 15 respectively) after mountains of work to clean them up. Days have turned into weeks, but my traffic numbers still hovered around their pre-penalty levels. Google amounted to 10-15% of our traffic (instead of the 60%+ it should have based on market share) while Yahoo and Bing supplied the rest. Occasionally, an interesting Google traffic result would weasel through, but it was a one-term recovery out of the possible thousands I was looking for.

I spent nights scouring the web looking for answers. Some webmasters saw their traffic return almost instantaneously. Others saw it take a month or as much as three months. There was no real rhyme or reason to these stories or the timeframes involved. The post commenters were beyond useless saying brilliant tidbits like, “you’ve cleared out all your links via disavow so you are basically starting back at zero you sorry spammer.” While I’m sure that’s the case with many a site, there are a good portion of webmasters who had a solid core of valuable links that got hidden by spammy links that were built by a shady SEO firm or just bad advise on link building techniques. Even for the most patient man in the world, the waiting can be a brutal exercise.

One night, I was digging away and stumbled across Marie Haynes’ article on Moz detailing the differences between penguin and a unnatural links penalty (brilliant article I highly recommend). I’ll admit the title was a bit perplexing at first since I always sandwiched these two together. It is a easy mistake to make since, on the surface, they both basically do the same thing — one penalizes you for shady links through a manual review by a Google employee (Unnatural links penalty) and the other is a algorithmic penalty for shady links levied by a bot (Penguin).

Parsing through the differences between the two led to my eureka moment. Just because Google has removed the manual penalty doesn’t mean there isn’t an algorihmic penalty still lingering on the site. True, you’ve done all the link clean-up to get back in Google’s good graces, but just because that Google evaluator flipped the switch on your site doesn’t mean the Googlebot is going to run right out and clear out the algorithmic penalty. Usually those get rolled out on some predetermined schedule on Google’s end. This is why webmasters were reporting recoveries from anywhere from a few days to three months. It all depends on when that next algorithm update goes into effect not when your manual spam action was revoked.

How do you know if you this applies to you? Did you see a big drop in traffic (30 to 50%) when the original Penguin update rolled out (April 24, 2012)? Then did you see another sizable drop sometime around when you received the message in your Google Webmaster Tools that they’d detected Unnatural Links on your site? If you didn’t see the Penguin drop, were you already operating under the Unnatural Links penalty at that time? If you can say yes to either of these, its a pretty solid bet that you’ve been infected by both penalties.

For a lot of you, the news of the lingering algorithm penalty won’t be terribly comforting. There is no defined end date that your site will return from the dark side of Google’s moon, and G’s engineers aren’t going to show their hand. The best advice I can give is to exercise extreme patience, use the downtime to continue building up a crop of high quality links and valuable content. Living under penalty isn’t fun, and I think Google plays the part of disapproving parent in a way telling us to sit in a corner and think about what you did. Much bigger fish than you have been made to wait out these prolonged algorithm lifts (ahem … J.C. Penny and even Google Chrome).

To all who fall underneath this umbrella, I wish you the best. I know its not an easy position to be in. Keep fighting the good fight, and your perseverance should pay off. Now if you are running a spammy site, operate in a heavily penalized genre (casinos, viagra, payday loans, etc.) or effectively disavowed all of your links, your traffic may not be coming back without you making some wide sweeping changes.

I’d love to hear your stories below from anyone who wants to share their experience with Google lifting a manual spam penalty, when traffic returned or if you are still waiting. Follow us on Twitter, Facebook or Google Plus for hopefully the final installment of this series — 301 redirecting a website with a manual penalty recently removed.