A Simple Guide to Optimizing Website Internal Linking Structure

By Shannon Dunn

Having a great internal linking strategy is essential for a website’s success, both for user experience and for SEO. The ranking and indexing of a site depend on a number of factors, the layout of site’s structure via main navigation and on-page internal linking being some of the most important aspects of optimization. Consideration of a site’s number and authority of backlinks also affect how search engines will prioritize pages.

This article is meant to address the issues faced with the distribution of link equity through overall site architecture as it relates to the depth of internal linking within the site. It will also provide a simple methodology to identify sections of the site by category that are either benefiting or suffering from the site’s structure due to the depth of pages and those with backlinks.

I’ll start out by covering the current state of internal linking recommendations, measuring link equity, faceted navigation, and other relevant pieces of the website architecture puzzle.

Lastly, I’ll be giving a methodology that focuses on analyzing categorical sections of a site that will hopefully help to make sense of internal linking optimizations in a simple format.

  1. Overview
    1. Internal Linking
    2. Backlinks
  2. Things to Consider for Internal Linking Strategies
  3. Website Internal Linking Analysis Methodology
    1. Using Google Sheets
    2. Pages by Crawl Depth and Number of Backlinks
    3. Pages by Crawl Depth and Number of Inlinks
  4. Recap of Possible Solutions

Let’s start by covering some of the basic concepts relevant to website structure and link equity.

Internal Linking

The fundamentals of site structure lie in the design and strategy of internal links, most critically in the main navigation of the site. The number of clicks from the Homepage (page depth) and internal links pointing to a page, determine that page’s importance within the site.  

This, in combination with backlinks, has been quantified with the metric Pagerank. There are many articles that give advice on calculating your site’s PR based on their own interpretation of Google’s algorithm: The Google Pagerank Algorithm and How It Works,  Calculate Internal PageRank, How to Calculate Pagerank and What to Do with It.


The quality and number of backlinks to your pages determine their ranking potential. We also know that pages linked from pages with backlinks receive link equity from their connection.

It’s important to note that both internal links and backlinks have a large impact on ranking in SERPs. Internal links can influence how Googlebot crawls your site, which impacts indexation, user experience, and how search engines view the hierarchy of your site, more so than a submitted XML sitemap.

Things to Consider for Internal Linking Strategies

  • Provide great user experience. This is a best practice for all SEO strategies, including internal linking. I.e. don’t put irrelevant links onto pages just to optimize for link equity.
  • Limit your faceted navigation and filters options to preserve link equity. Read more here for large sites.
  • Paginated Pages should contain rel=next and rel=prev tags to improve indexation for the main page in the sequence.
  • Nofollow tags can’t re-distribute link equity among internal links. For example, if there are 10 links on a page that receives 100 units of link equity and you nofollow 2 links,  the other 8 links will still only pass 80 units instead of the full 100 units.
  • Remove redirects/redirect chains from internal linking that dilute link equity.
  • Both backlinks and internal links affect ranking, the number of inlinks pointing to pages on the site being just as important.
  • Measuring the impact of changes is still unscientific, without products such as ODN or you own interpretation of Google’s algorithm for Pagerank. That doesn’t mean there are guidelines we can’t still follow with the above.

A Simple Methodology for Identifying Internal Linking Opportunities

This process is useful for quickly identifying valuable pages that may be unintentionally hidden deeper within the website. By moving these pages into better positions within the site architecture, you are sending strong signals to Google that these pages are important.

What you will need to do this methodology: Screaming Frog, Ahrefs, and Google Sheets or Excel. The most time-consuming part of this process will be bucketing your site’s content together into sections and then later deciding which pages from each section to prioritize.

Pages located deeper within your site that are critical to business goals should be linked within 3 clicks of the homepage. These important pages could be optimized landings pages, other pages within a defined conversion funnel, and any other pages on the site that contribute heavily to overall business goals.

The methodology for creating a spreadsheet and visualisation is an estimation of which areas of the website can be improved in terms of internal linking and backlinks. Not all backlinks are equal, given that a backlink from a site with a higher domain authority will be stronger than a backlink from a spammy website.

  1. Crawl Site with Screaming Frog

I’d advise excluding images, CSS, and JS files from your crawl, as these aren’t necessary.

  1. Export “Internal All”

Isolate the Address column, the Crawl Depth column (Crawl Depth is the number of clicks from the start page.), Status Code, and the Inlinks column (The number of internal links pointing to a URL).

  1. Export Ahrefs Best Pages by Backlinks

Then create a new column for backlinks to your pages and perform a vlookup to match the number of backlinks to the respective page.

Make sure you are using the column ‘Dofollow’ in the Ahrefs export.

  1. Categorize URLs into Site Sections

This is basically organizing the pages of your site into categories. You can go as in depth as you want, but to get the most value out of this process consider keyword targeting in addition to the content topic when grouping URLs.

The process is much easier if your URLs already contain subfolders that indicate categorical structure to your site. However, if your URLs paths don’t follow distinguishable naming conventions, you can also consider using the page title as a way to quickly categorize.

You will need to make another column for categories and label URLs by their category. To make it quicker, filter the address column for the category keyword, then copy and paste your label into the category column for all URLs that apply.

Using Google Sheets to Organize the Data by Category

After breaking down the site into categories, you can create a table to visualize how far deep into the site they are internally linked. In combination with backlinks, inlinks, and status codes, we can first identify pages that are located farther in the site with backlinks and also investigate the inlinks and status code for those pages.

Google Sheets is a very practical way to analyze, share, and visualize your data. With the data organized from excel, you can copy paste them into google sheets and create a pivot table from the results.

Essentially, for internal linking purposes, a page can receive better ranking potential from the following: More internal links, backlinks, a status code of 200, and a page depth of within 1-3 clicks from the Homepage. While these attributes are not everything a pages needs for optimization, they are significant pieces of the SEO puzzle.

There are several ways to use your data with SEO benefits in mind:  

  1. Find pages within a section that have more backlinks and prioritize linking these pages within 1-3 clicks from the Homepage or from the internal navigation within the appropriate section to use the benefit of the link equity for ranking.
  2. Identify pages that have a high amount of inlinks and determine if they are important/have ranking potential. If not, then remove them from the navigation or where they are linked so that they are not prioritized for indexation and further dilute link equity.
  3. Audit pages with low amounts of inlinks to determine if they are important/have ranking potential and either put them into the navigation or ensure they are linked on pages in the appropriate section.

Investigating Pages by Crawl Depth and Number of Backlinks

Below, I created a pivot table from the data showing Category as the columns, Crawl Depth as the rows, and Backlinks as the values within the table. By filtering for Backlinks on Categories past 3 clicks from the Homepage, we can determine which sections would create benefits for the site and help with ranking those pages if internally linked higher in the site architecture.

In this particular example, we can see the section Bags has a sum of 73 backlinks on pages located 7 clicks from the Homepage. This gives us a starting point in re-adjusting the site’s internal linking structure.

For reporting, creating a scatter plot provides easy visualizations for backlinks by crawl depth within the site.

In order to review the specific pages in the Bags section that are 4-7 clicks from the homepage, we can backtrack to our pivot table and filter the Category for Bags and Crawl Depth.

We can now quickly see the two URLs in the Bags section we can consider as priorities for linking higher in the website, or even the main navigation if appropriate. It’s also good to view the status code of these URLs with high numbers of backlinks as it will influence the link equity given to those pages.

If these pages are old and outdated, consider 301 redirecting these pages or canonicalize them to similar products/category pages that will help more important pages to rank.

Investigating Pages by Crawl Depth and Number of Inlinks

Using our pivot table, we can both concentrate on finding sections/pages with either a high amount of inlinks within 1-3 clicks from the Homepage or with low number of inlinks.

Filter by the number of inlinks descending to review if there are pages that are being prioritized on the site that do not belong.

Here we can see that many of the most linked pages are products that are taking priority over category pages and do not necessarily have the most backlinks pointing to them.

At the category level, we can create a table similar to earlier that shows the sum of inlinks by their crawl depth. By filtering the table for 0-20 inlinks, we can see that there are some sections that are not being linked to within the site very well.

If any of these pages within these sections are important to the site, they should be added into the internal navigation or linked within the body content higher within the site’s architecture.

Recap of Possible Solutions

  • Prioritize important pages by ensuring they can be crawled easily within the first 1-3 clicks from the Homepage.
  • Increase the flow of link equity on the site by linking to pages with high numbers of backlinks.
  • Create more inlinks for important pages by including them in the main navigation or by including more internal linking within the body content.  (I.g. a blog article can be linked internally by other relevant blog articles for reference in the body content.)
  • 301 redirect pages with high amounts of backlinks that are outdated/no longer valuable to user experience on the website/not a high amount of organic traffic.
  • Consolidate site sections if many pages overlap in topic/intent by canonicalizing or by 301 redirecting.
  • Consider adding breadcrumbs for additional internal linking and site structure.