Direct traffic can encompass a wide range of sources, including those you would have liked to have tracked in analytics. A drop in traffic from a particular source does not necessarily mean a drop in traffic. It could indicate a case in which that source ended up being categorized under Direct traffic. The best advice is - proactively use tracking parameters in cases where you may be risking not properly seeing traffic. There is actually a nice infographic showing the main factors impacting traffic. I use it sometimes to solve the current issues. Taking the right steps to address potentially miscategorized traffic, as well as being upfront with clients about the causes, can help to mitigate problems.

One of the things that can slow-bleed the traffic from your site is the quality (or lack thereof) of the content you publish on your site. Previous Google updates like Panda have already been released specifically to deal with the issue of low-quality content on websites. Long story short: Panda intended to stop sites with bad content from appearing in the search results.
The Forums – yes, I know some bloggers are telling you that you can not get anything from the Forums, but I can prove them wrong. One example: I met one of my dear blogging friends on a Forum way before I started blogging. She has been helping me since. Instead of struggling with some newbie mistakes, I skipped most of them and went straight for success. Most forums allow links in signatures – use it!

Consumers only have so much attention and so much money — and for each, they set a “budget” for how much they want to spend with the brands that are important to them. Consumers invest their attention and money into big promotions. Typically, big promos have big results for the retailer, but the flip side is that the promo has emptied the consumers’ budget for attention and money. If the promo is big enough, it even entices some consumers to overspend a little bit (or a lot). When consumers have expended or exceeded their budget, they tend to engage with your brand less. They become immune to marketing messages and spend fewer dollars.
Now in your reconsideration request make sure you are honest and tell Google everything that the prior agency was up too. Be sure to include all Excel information of removed links and say you are going to make an ongoing effort to remove everything negative. It is common knowledge that Google may not accept your first reconsideration request, so it may take a few times.
Note: Google made a change a few years ago to how they track keywords and it has had a big impact on the discovery process. Before the change, Google would show which keywords consumers were using to find your website, making it easy to understand where and how your website was ranking. Google changed their tracking system so that any users who are logged into a Google account while searching will no longer have their keywords tracked as their Google activity remains encrypted. Due to this, when looking at Organic Traffic reports you will see (not provided) as a keyword throughout the reports – this often makes up over 90% of organic traffic and requires us to dig a bit more creatively to find what we need.
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We used to like best to see a fairly balanced mix, back when there were mostly just three sources: Organic, Direct, and Referral. Organic Search traffic is a good sign of general site health, it’s usually the top source of conversions, and it generally shows great ROI. Direct traffic is often the people who love your site or are coming back to buy after they found you in some other way. These two groups of visitors are probably the ones that bring you the most sales or leads.
For our client: We were lucky enough to remove most from the prior agency outreach, we also went directly to many webmasters in which we wanted to remove links. We did not use the Disavow tool as it was not around when we completed this link cleanup, but we all know it has been said that if you are going to use the Disavow Tool to use it with caution.
Looking back at our lab site, we can see that Organic Search is doing well for us. However, if we put a little effort into social media, we’d probably see growth in that sector — and a bigger pie. We’ve got some strong referrals (and high quality links that improve our search presence), but if we put some work into building more of those links, we’d probably see more referral traffic and, again, a bigger pie. Should we add paid search? For this site, no. It’s part of our community service and has little revenue potential, so we wouldn’t see much ROI from ads.
To sum up all of this information, even organic traffic, like direct traffic, has some gray areas. For the most part, though, organic traffic is driven by SEO. The better you are ranking for competitive keywords, the more organic traffic will result. Websites that consistently create content optimized for search will see a steady increase in organic search traffic and improved positioning in the search results. As a marketer, it is important to look at your keywords and high-ranking pages to identify new SEO opportunities each month.  
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