13 min read · Technical SEO · Last updated July 2026
Quick answer: Ahrefs Site Audit crawls your entire website and scores it across 100+ technical checks. Run a crawl, triage issues by severity (Critical first, then Warnings, then Notices), fix the highest-impact problems, and re-crawl to confirm. A health score above 80 is solid; anything below 60 means technical problems are actively limiting your rankings.
Introduction
Most sites have technical problems their owners never discover. A JavaScript error silently blocking an entire category. Thin product pages getting indexed and cannibalising stronger content. Three thousand internal links pointing to a URL that 301-redirects twice before landing somewhere useful.
Ahrefs Site Audit surfaces all of it — but the tool only delivers value if you know what to act on. With 47 issue types and potentially hundreds of thousands of flagged URLs, knowing where to start is the real skill.
This guide walks through every major section of Ahrefs Site Audit, explains what the data actually means, and shows you which fixes move rankings.
What you’ll learn:
– How Ahrefs Site Audit crawls your site and calculates its health score
– How to read the crawl overview and find your highest-priority issues
– How to diagnose internal linking gaps, broken pages, and duplicate content
– How to compare crawls over time to track technical SEO progress
Table of Contents
- Setting Up Your First Crawl
- Understanding the Health Score
- Crawl Overview: Reading the Dashboard
- Critical Issues to Fix First
- Internal Linking Gaps
- Duplicate Content and Canonicalization
- Coverage and Indexability Issues
- Comparing Crawls Over Time
- Prioritising Your Fix List
- Frequently Asked Questions
Setting Up Your First Crawl
Before you get any data, you need to configure the crawl correctly. A misconfigured crawl gives you inaccurate issue counts and misses entire sections of your site.
Crawl scope: Set the scope to your entire domain, not a subdirectory, unless you are specifically auditing a section. If your blog lives at /blog/ and your main site at /, crawl both together.
Crawl source: Ahrefs can crawl via its own bot or through Google Search Console integration. Use the GSC integration if you want to see coverage data aligned with what Google actually knows about your site — this is the more valuable setup for most sites.
JavaScript rendering: Enable JavaScript crawling if your site uses a JS framework. Without it, Ahrefs misses content that only renders client-side — including navigation menus, product descriptions, and entire page sections.
Crawl rate: Set this conservatively for shared hosting or WordPress sites. Aggressive crawl rates trigger rate limiting, which produces incomplete data.
Understanding the Health Score
The Ahrefs health score is a percentage representing the share of internal URLs without errors. A 90% score means 10% of crawled pages have at least one critical issue or warning.
The score is useful as a trend indicator, not an absolute benchmark. A new e-commerce site with 500 products might legitimately score 95%. A large news site with 500,000 pages and complex redirect chains might score 72% — and still perform well because the issues affecting that 28% are low-priority.
What actually matters:
– Critical errors on indexable pages (these actively harm rankings)
– Warnings on high-traffic or high-value pages (prioritise by page importance)
– Health score trend across crawls (improving, stable, or declining)
Ahrefs Health Score Meter
Enter your site’s health score to see what it means and what to prioritise.
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Crawl Overview: Reading the Dashboard
The crawl overview gives you a snapshot across six categories: Errors, Warnings, Notices, Crawled pages, Non-indexable pages, and Links.
The number that matters most: look at the ratio of crawled pages to indexed pages. If Ahrefs crawled 8,400 URLs but you expect only 3,200 to be indexed, you have a bloat problem. Excess indexable URLs dilute crawl budget and cause Google to waste time on low-value pages.
Crawl distribution: check how many pages are in each content type. If 60% of your crawled URLs are parameter variants of product pages, you have a URL parameter problem — not a content problem.
Response codes breakdown: the response codes chart shows what percentage of your URLs return 200, 3xx, 4xx, or 5xx. Any site with more than 2% 4xx URLs has a broken internal linking problem worth fixing immediately.
Critical Issues to Fix First
Ahrefs flags Critical errors that directly impact crawlability, indexability, or page signals. These are not cosmetic — they are ranking problems.
Broken pages (4xx): Internal links pointing to 404 or 410 pages leak PageRank and waste crawl budget. Export the list, check whether each broken URL should be restored or redirected, and implement 301 redirects to the nearest relevant live page.
3xx redirect chains: A redirect chain is any URL that redirects more than once before reaching its destination. Each hop loses approximately 15% of link equity. Ahrefs flags chains of 3 or more as Critical. Fix by updating the source URL to point directly to the final destination.
Pages returning 5xx: Server errors block Google from crawling those pages entirely. If you see 5xx errors in your crawl, check your server logs immediately — this is often a hosting or plugin conflict causing intermittent failures.
Noindexed pages receiving backlinks: This is a common mistake. A page has noindex but still has 47 external backlinks pointing at it. All that link equity disappears. Either remove the noindex tag or set up a redirect to a canonical indexable page.
Key takeaway: Fix 4xx errors and redirect chains before anything else — they are losing you link equity right now.
Internal Linking Gaps
The internal links report in Ahrefs Site Audit is one of its most underused features. It shows you pages with few or no internal links pointing to them — what the industry calls “orphan pages.”
Why orphan pages matter: Google discovers pages primarily through crawling internal links. If a page has zero internal links, Google may never find it, or may deprioritise it as low-value. Orphan pages also receive no PageRank from other pages on your site.
Finding orphan pages in Ahrefs:
1. Go to Site Audit → Internal pages
2. Filter by “Incoming internal links” = 0
3. Cross-reference against pages that have organic traffic or backlinks
Pages with external backlinks but no internal links are priority fixes — they receive link equity from outside but cannot distribute it internally.
The “one deep link” trap: many sites technically link to pages but only from a single location — often a footer or sitemap. Google values contextual links within body content far more than navigational links. A page with 200 links from footers but 0 body content links is effectively an orphan for ranking purposes.
Aim for your most important pages to have at least 3-5 contextual internal links from relevant content.
Site Audit Issue Priority Matrix
Rate each issue type by impact and effort to see your optimal fix order.
| Issue Type | Severity | Ranking Impact | Fix Effort | Priority |
|---|---|---|---|---|
| Broken internal links (4xx) | Critical | High | Low | P1 |
| Redirect chains (3+ hops) | Critical | High | Medium | P1 |
| Noindexed pages with backlinks | Critical | High | Low | P1 |
| Duplicate title tags | Warning | Medium | Low | P2 |
| Missing meta descriptions | Warning | Low | Low | P2 |
| Orphan pages | Warning | Medium | Medium | P2 |
| Images missing alt text | Notice | Low | Low | P3 |
| Slow page speed | Notice | Medium | High | P3 |
Duplicate Content and Canonicalization
Duplicate content is the most common technical issue on e-commerce and CMS-driven sites. Ahrefs detects it by comparing page content similarity across your crawled URLs.
The four types Ahrefs flags:
1. Exact duplicates — identical HTML content on two or more URLs
2. Near-duplicates — pages that share 80%+ of their content (e.g., size/colour variants)
3. Pages with duplicate titles — different URLs, same <title> tag
4. Pages with duplicate H1s — different URLs, same primary heading
Near-duplicates are the most common on product sites. A shirt available in 12 colours and 5 sizes can generate 60 near-identical URLs. Without canonicalization, you are forcing Google to choose which version to index — and it often chooses wrong.
Fixing duplicate content:
– For parameter variants: add rel="canonical" pointing to the primary URL
– For paginated series: canonical each page to itself (do not self-referential canonical to page 1 — this hides pagination from Google)
– For exact duplicates: consolidate with a 301 redirect to the definitive URL
– For print versions: add noindex to print-specific URLs
The Ahrefs canonical report shows you pages where the canonical tag points to a URL that itself has issues — a “broken canonical chain.” These are common after migrations and cause Google to ignore your canonicalization signals entirely.
Coverage and Indexability Issues
The indexability report in Ahrefs groups your crawled URLs into:
– Indexable pages
– Non-indexable pages (with reason)
– Unknown (usually server errors or blocked by robots.txt)
Key ratio to check: If more than 30% of your crawled URLs are non-indexable, you need to understand why. Some non-indexability is intentional (thank-you pages, admin pages, duplicate parameter URLs). Some is accidental — pages you want Google to index that somehow ended up noindexed.
Common accidental noindex sources:
– WordPress plugins that noindex certain post types by default
– Staging environments where someone removed noindex before launch
– Tag and author archive pages that were noindexed for thin content but now have valuable content
– Product filter pages that are blocked by both noindex AND disallow (double-blocking, wasteful but harmless — except for crawl budget)
Comparing Crawls Over Time
The crawl comparison feature is where Ahrefs earns its cost for large sites. Run a crawl before a site migration, CMS upgrade, or template change, then run another after. The diff shows you exactly what broke.
What to compare:
– Health score delta (did your score go up or down?)
– New issues introduced (did the migration create new 404s or redirect chains?)
– Resolved issues (did last month’s fixes actually work?)
– Page count changes (did you accidentally noindex a category?)
Set up scheduled crawls — weekly for active sites, monthly for low-change sites — so you have a continuous health record. When something breaks in organic traffic, the crawl comparison tells you exactly when the technical issue appeared.
Key takeaway: Crawl comparison data is your audit trail. It proves whether fixes worked and when problems started — invaluable for diagnosing traffic drops.
Prioritising Your Fix List
After a full audit, you might have 50,000 flagged URLs across 30 issue types. The mistake is trying to fix everything. The skill is fixing the right things in the right order.
The prioritisation framework:
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Severity × Page value: a Critical error on a page with 500 monthly visitors is worth 10x more than the same error on a page with 5 visitors. Export issues, join with GSC traffic data, sort by (severity score × clicks).
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Bulk fixes first: if 3,000 URLs all have the same issue (e.g., missing H1 tags from a template bug), that is one fix — a template change — not 3,000 individual tasks.
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Crawl budget impact: fixes that reduce the number of crawlable low-value URLs often have compounding effects. Removing 10,000 parameter URLs from the crawl means Google spends more budget on your important pages.
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Link equity impact: fixes that recover lost link equity (broken redirects, noindexed backlinked pages) have immediate and measurable impact. Prioritise these when you have clear evidence of link equity loss.
Track your progress in Ahrefs by comparing consecutive crawls. Every fixed issue should reduce your issue count — if it does not, check whether your fix was implemented correctly.
Frequently Asked Questions
How often should I run an Ahrefs Site Audit?
For active sites publishing content or undergoing changes, run weekly crawls. For stable sites, monthly is sufficient. Always run a crawl before and after any significant technical change — migrations, redesigns, plugin updates.
What is a good health score in Ahrefs?
80+ is considered healthy for most sites. 90+ is excellent. Below 70 indicates significant technical issues that are likely limiting organic performance. But the absolute number matters less than the trend — a site moving from 65 to 80 over three months is making real progress.
Can Ahrefs Site Audit crawl JavaScript-rendered content?
Yes, but you need to enable JavaScript rendering in the crawl settings. Without this, Ahrefs crawls the raw HTML response, which misses anything rendered by JavaScript. This is critical for sites built with React, Vue, Angular, or Next.js.
What is the difference between Ahrefs Site Audit and Google Search Console coverage?
Ahrefs crawls your site as a bot and flags technical issues based on its own rules. GSC Coverage shows what Google has actually indexed — its own crawl of your site. Use both together: Ahrefs to proactively find issues, GSC to see how Google has responded to them.
How do I fix the “orphan page” issue in Ahrefs?
Find pages with zero incoming internal links via Site Audit → Internal pages → filter by “Incoming links = 0”. For each orphan page, identify the most relevant content on your site and add a contextual internal link to that orphan page from the body content of that related page.
Should I fix all Warning-level issues?
Not all Warnings are equal. Prioritise Warnings on your highest-traffic and highest-value pages first. Some Warning-level issues (like missing meta descriptions on paginated pages) have near-zero ranking impact and can be deprioritised indefinitely.
Conclusion
Ahrefs Site Audit is the most complete technical SEO auditing tool available, but its value is proportional to how systematically you use it. Run regular crawls, triage by severity and page value, fix in bulk wherever possible, and compare crawls to measure progress.
The sites that pull ahead technically are not the ones that fix every issue — they are the ones that fix the right issues fast and keep fixing them consistently.
Let Ignited Nepal Handle This
Running Ahrefs audits, triaging 50,000 flagged URLs, and coordinating fixes across dev and content teams is a full-time job. Our team does this daily for clients across Nepal, Australia, UAE, and beyond.
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Written by the Ignited Nepal SEO team. We build organic search systems for businesses across Nepal, Australia, UAE, USA, UK, and beyond. ignitednepal.com