How to conduct a comprehensive site structure analysis in Ahrefs for better SEO

If you're serious about SEO, but tired of vague advice about “optimizing your website,” this one's for you. Maybe your rankings are stagnant, or you suspect your site structure is a mess. Either way, a hands-on site structure analysis can clear up what’s really going on. You don't need to be a developer or a full-time SEO nerd to get value out of this—just some curiosity and a willingness to dig in.

We're going to walk through how to use Ahrefs to actually see what's happening with your site's structure, spot the real problems, and take action that matters. No fluff, no busy work.

Step 1: Crawl Your Site with Ahrefs Site Audit

Before you do anything else, you need a complete picture of your site. That means crawling it—just like Google would.

  • Go to Site Audit: In Ahrefs, click on “Site Audit.”
  • Add your project: If you haven't already, set up your domain. Use the “Add Project” button.
  • Configure crawling settings:
    • Enter your root domain (e.g., example.com).
    • Choose “Crawl all subdomains” if you use them.
    • Set the crawl source to “Website” for the most accurate picture.
    • Adjust crawl speed if your host is touchy (don’t get yourself banned).
  • Start the crawl: Hit “Start” and go do something else—this may take a while on big sites.

Pro tip: If your site requires logins or has weird JavaScript navigation, accept that Ahrefs might not see everything exactly as a user would. For most “normal” marketing sites, the crawl is plenty.

Step 2: Visualize Your Site Structure

Sitemaps and menus only tell half the story. You want to see how your pages actually connect.

  • Head to the Structure Explorer: Once your crawl finishes, go to “Structure Explorer.”
  • Try the ‘Tree View’: This gives you a folder-like view based on URLs. You’ll quickly spot:
    • Deeply buried pages (e.g., /blog/2022/12/15/forgotten-post)
    • Orphan pages that don’t fit anywhere
    • Oddball URL structures
  • Switch to ‘Directory Depth’: This lets you see how many clicks it takes to reach each page from the homepage. Pages buried deep rarely get traffic or rank.

What to actually look for: - Are your important pages (money pages, key content) close to the homepage? - Do you have giant “flat” sections with hundreds of similar pages? - Are your URLs organized in a way that makes sense to a human?

Ignore: Fancy-looking graphs that don’t help you make decisions. The goal is to spot problems, not print pretty charts for a boss.

Step 3: Identify Orphan Pages and Crawl Issues

Orphan pages are pages with no internal links pointing to them. Search engines struggle to find these, so they rarely rank.

  • Check the “Orphan Pages” report: In Site Audit, go to “Internal Pages” and filter for “Orphan.”
  • Decide if you care:
    • Some orphans are junk (old landing pages, test pages).
    • But if you see important content here, it needs links—fast.

Other crawl issues to check: - 4XX/5XX errors: Broken pages waste crawl budget. - Redirect chains: Multiple redirects slow things down and waste link equity. - Non-indexable pages: Are there pages that should be indexed but aren’t? (Check “Indexability” column.)

Pro tip: Not every error is urgent. Focus on pages that actually matter for your business or users.

Step 4: Analyze Internal Linking

Internal links are your secret weapon. They help Google (and visitors) understand what matters and how pages relate.

  • Go to the “Internal Links” report: See which pages have the most and least internal links.
  • Look for these problems:
    • Important pages with only a couple of links pointing to them.
    • Pages with tons of links but low value (e.g., tag archives, boilerplate).
    • “Dead ends”—pages with no outgoing links.
  • Check anchor text: Are you using the same keyword-stuffed anchor everywhere? Mix it up for natural linking.

What actually works: - Add relevant internal links from high-traffic pages to your most important, underlinked pages. - Use descriptive, natural anchor text. “Read more here” is fine, but “Guide to blue widgets” is better if it fits.

Ignore: Trying to force hundreds of exact-match anchors. Google sees through this, and it’s annoying for users.

Step 5: Evaluate Site Depth and Click Distance

Pages buried more than 3-4 clicks from the homepage might as well be invisible for most users and for Google.

  • Use the “Depth” column in Structure Explorer: Sort by depth, highest first.
  • Flag key pages buried too deep: If your best guides or product pages take five clicks to reach, that’s a problem.
  • Plan to surface them: Add links from navigation, hub pages, or popular blog posts.

What to ignore: Don’t obsess over getting every single page to depth 1 or 2. Some pages (old blog posts, legal disclaimers) can live deeper. Focus on what drives revenue or traffic.

Step 6: Spot Duplicate Content and Thin Pages

Duplicate or near-duplicate content confuses search engines. Thin pages (with little unique info) don’t help you rank.

  • Check the “Content Quality” report: Ahrefs will flag duplicates and thin content.
  • Review the flagged pages:
    • Are there real duplicates (e.g., /about and /about-us)?
    • Are there pages with barely any text?
    • Do you have multiple variations of near-identical product/category pages?
  • Decide what to fix, combine, or delete.

Pro tip: Don’t stress about things like privacy policies being “duplicate”—Google expects that. Focus on unique pages that should be ranking.

Step 7: Review Your Site’s Hierarchy and Navigation

This is the “common sense” part. Look for these red flags:

  • Important pages not linked in main navigation.
  • Navigation cluttered with dozens of low-value links.
  • Categories that don’t match how users actually search.
  • No clear path from homepage to key sections.

How to fix: - Simplify navigation to highlight your best content and money pages. - Group related content under clear categories. - Remove or demote unimportant links.

Ignore: Overcomplicating things. If a “site silo” structure feels forced or makes navigation harder, skip it. Users come first.

Step 8: Prioritize and Take Action

At this point, you’ll have a laundry list of potential issues. Don’t try to fix everything at once.

  • Rank fixes by impact:
    • Will adding internal links to a revenue page move the needle? Do that first.
    • Broken links and orphaned important pages? Fix them next.
    • Thin content and deep pages? Batch these after big wins.
  • Track changes: Make a simple spreadsheet or use your project management tool—just don’t lose track.

Pro tip: You’ll never “finish” site structure. It’s an ongoing process. Aim for better, not perfect.

Honest Takes & Common Pitfalls

  • Don’t chase every warning: Some “errors” in Ahrefs are just noise.
  • Automated suggestions ≠ good advice: Use your brain, not just the tool.
  • Site structure ≠ magic bullet: If your content is thin or irrelevant, no amount of perfect structure will save it.
  • Be wary of endless tinkering: Ship improvements, don’t get stuck in analysis mode forever.

Wrapping Up: Keep It Simple, Iterate Often

Analyzing your site structure with Ahrefs isn’t about chasing perfection or ticking every box. It’s about making it easier for users and search engines to find what matters on your site. Start with the basics, fix what you can, and revisit every few months. SEO is a long game—keep moving, and don’t let the perfect be the enemy of the good.