Website SEO health check: how to find and fix every issue holding you back

What is an SEO health check?

An SEO health check is a systematic audit of your website that looks at every factor affecting how Google discovers, crawls, indexes, and ranks your pages. It covers three broad areas: technical SEO, on-page optimisation, and backlinks. Together, those three areas tell you whether your site is structurally sound enough to compete in search results, whether your content is optimised correctly, and whether other websites trust you enough to link to you.

The output of a health check is a prioritised list of issues. A good audit does not just surface problems, it scores them by severity and tells you which ones to fix first. Spending a week fixing broken image alt text while a crawl budget issue is blocking 40% of your pages from indexing is a common mistake that a proper audit prevents.

Most SEO site audit tools assign a site health score, typically out of 100. This score reflects the proportion of pages that pass technical checks rather than a direct measure of ranking potential. A score of 65 does not mean your site is bad at SEO, it means the tool found a significant number of issues across your crawled pages. The score is a starting point, not a verdict.

Running a website SEO health check is the right first step before you start creating content, building links, or paying for paid traffic. If your site has crawl errors, broken redirects, or duplicate content issues, every other SEO activity you do sits on top of a leaking foundation.

How to run a website SEO health check

A thorough health check works through six areas in sequence: crawl and indexation, technical performance, on-page signals, content quality, backlinks, and user experience. Running them in this order matters because some later issues only become relevant once the earlier, structural ones are confirmed as clean.

Step 1: crawl your site and check indexation

Start with a crawl. Tools such as Semrush Site Audit, Ahrefs Site Audit, and Google Search Console will scan your pages and return a list of discovered URLs alongside status codes. Your first task is confirming that the pages you want indexed are indexed, and the pages you do not want indexed are excluded.

1. Open Google Search Console and navigate to the Coverage or Indexing report. Look at the count of indexed pages versus the number of URLs Google has found but not indexed, and the reason Google gives for excluding each one.
2. Check your XML sitemap. It should contain every page you want indexed and nothing else, no 301 redirects, no 404s, no noindex pages, and no pages blocked by robots.txt.
3. Review your robots.txt file directly at yourdomain.com/robots.txt. Confirm it is not blocking any directory or URL pattern that should be crawlable. A mistakenly broad disallow rule is one of the most damaging issues a site can have, and it is invisible to users.
4. Check for orphan pages, pages that exist on your site but have no internal links pointing to them. Orphaned pages are rarely indexed reliably because Google's crawler discovers new pages primarily by following links.

Step 2: technical performance checks

Once you are satisfied with crawlability and indexation, move to technical performance. This layer covers the factors that affect how well Google can read your pages and how quickly they load for visitors.

1. Run a Core Web Vitals check using Google Search Console's Core Web Vitals report or PageSpeed Insights. Look for pages that fail the Largest Contentful Paint, Cumulative Layout Shift, or Interaction to Next Paint thresholds. Pages in the red or amber zones are at a ranking disadvantage on mobile searches.
2. Check your HTTPS status. Every page should load over HTTPS with a valid certificate. Mixed-content warnings, where a secure page loads some assets over HTTP, can suppress rankings and trigger browser security warnings for visitors.
3. Review redirect chains. A redirect chain occurs when page A redirects to page B, which redirects to page C. Each hop dilutes the link equity passed along the chain and slows load times. Audit for chains longer than one hop and flatten them where possible.
4. Check for canonical tag errors. Pages with self-referencing canonicals should match the exact URL Google is indexing. Pages with canonicals pointing to the wrong URL are telling Google to ignore them entirely.
5. Audit your page titles and meta descriptions for duplicates. Duplicate titles are a common technical issue that tells Google two or more pages are competing for the same query, splitting any ranking signal between them.

Step 3: on-page optimisation audit

On-page issues are fixable within your CMS or code without waiting for Google to recrawl. This makes them some of the fastest wins available after an audit.

1. Check every page for a single H1 tag. Missing H1s leave Google without a clear signal about the page's primary topic. Multiple H1s on one page are a structural mistake that can confuse both the crawler and the reader.
2. Review title tag lengths. Titles truncated in search results lose their descriptive function. Aim for 50 to 60 characters for every important page.
3. Audit image alt text. Every image should have a descriptive alt attribute. Missing alt text is both an accessibility failure and a lost on-page signal for pages where images are central to the content.
4. Check for thin content. Pages with fewer than 300 words rarely rank for competitive queries unless they serve a very specific navigational intent. A thin content audit flags pages that could be merged, expanded, or redirected to stronger versions.
5. Identify keyword cannibalisation. If two or more pages on your site target the same primary keyword, they will compete against each other in Google's results. An audit tool will surface pages with identical or very similar title tags and meta descriptions that suggest this overlap.

Step 4: backlink profile review

Your backlink profile is the external half of your SEO health. Tools like Ahrefs and Semrush pull backlink data from their own indices, showing you which domains link to your site, the quality of those domains, and whether any links could be doing damage rather than good.

1. Check your referring domain count and the trend over time. A growing referring domain count is a positive signal. A sharp drop, especially one that correlates with a traffic decline, suggests a manual action or algorithmic penalty affecting your link profile.
2. Review your anchor text distribution. An anchor text profile dominated by exact-match keyword anchors looks manipulative to Google's link spam systems. A healthy profile has a mix of brand name anchors, generic anchors, and partial-match keyword anchors.
3. Identify and flag toxic or spammy links. Ahrefs and Semrush both assign toxicity or spam scores to linking domains. Links from link farms, private blog networks, or sites with unrelated or low-quality content can suppress your domain's authority.
4. Check for broken backlinks. If external sites link to a page on your domain that no longer exists, that link is sending visitors and link equity to a 404 error. Identify these and either restore the page or add a 301 redirect from the old URL to the closest current equivalent.

Step 5: user experience signals

Google treats certain user behaviour signals as ranking inputs. A site that loads slowly, is hard to navigate on a phone, or puts content behind intrusive pop-ups will underperform against a technically cleaner competitor, even if both have similar content quality and backlinks.

1. Test your site on a mobile device. Navigate through your most important pages and check whether text is readable without zooming, whether buttons are large enough to tap accurately, and whether the layout breaks at any point. Google indexes and ranks the mobile version of your site first.
2. Measure your mobile page speed using PageSpeed Insights. The tool breaks down specific opportunities for improvement, from image compression to unused JavaScript, and scores each one by its estimated impact on load time.
3. Check for intrusive interstitials. Pop-ups that cover the main content on mobile immediately after a visitor arrives from a search result can attract a ranking penalty. Cookie consent banners that comply with legal standards are excluded from this rule.

Best tools for an SEO health check

The right tool depends on your budget, the size of your site, and the depth of reporting you need. Paid platforms give you more pages crawled, more historical data, and sharper competitive context. Free tools are enough to identify the most serious issues on a small or medium-sized site.

Semrush Site Audit

Semrush Site Audit is one of the most widely used SEO health check tools for businesses and agencies. It crawls up to a configurable number of pages, assigns a site health score out of 100, and categorises all issues as errors, warnings, or notices. Each issue includes an explanation and a recommended fix, which makes the report accessible to someone running their first audit. You can schedule recurring crawls so the tool emails you whenever new issues appear. Semrush also integrates its audit data with its keyword ranking and backlink tools, so you can move between technical health and competitive performance without switching platforms. You can explore Semrush at Semrush.

Ahrefs Site Audit

Ahrefs Site Audit is the strongest option if you want depth in crawl data alongside Ahrefs' industry-leading backlink index. Its health score works similarly to Semrush's, but the platform is particularly strong for identifying internal linking gaps, orphan pages, and crawl depth issues. The data visualisation for internal link flow is one of the clearest in any audit tool and helps you see at a glance which parts of your site are well-connected and which are isolated. Ahrefs also highlights pages that are receiving significant backlinks but performing poorly in search, which is a high-value audit finding. See the full review at Ahrefs.

Google Search Console

Google Search Console is the only tool that shows you exactly what Google itself has discovered, indexed, and flagged on your site. It is free, has no page limit, and covers Core Web Vitals, manual actions, index coverage, and mobile usability from Google's own perspective. For any site owner running their first SEO health check, Search Console is the right starting point because the data is definitive rather than an approximation. The limitation is that it does not crawl your site in real time, it reflects what Google has discovered through its own crawl schedule, which may lag several days behind changes you make. Access it at Google Analytics and pair it with Search Console for a fuller picture of organic performance.

Rank Math

For WordPress sites, Rank Math is a plugin that performs on-page SEO audits at the page level as you edit or publish content. It scores each post and page against a checklist of on-page factors, including keyword in title, meta description length, internal links, alt text, and readability, and gives a score out of 100. It does not replace a full technical site audit, but it catches on-page issues before they become systemic. Rank Math also integrates with Google Search Console to pull keyword and ranking data directly into the WordPress dashboard. Review the tool at Rank Math.

Surfer SEO

Surfer SEO focuses on on-page optimisation rather than technical crawling. Its Content Audit feature analyses your existing pages against the top-ranking competitors for their target keyword and identifies gaps in word count, keyword usage, heading structure, and semantic coverage. This makes it particularly useful for the content quality phase of an SEO health check, where you want to know whether your pages are as complete and well-structured as the ones outranking them. Explore Surfer SEO at Surfer SEO.

HubSpot Website Grader

HubSpot's free website grader provides a quick four-area score covering performance, mobile readiness, SEO basics, and security. It does not crawl beyond the URL you submit, so it is not a substitute for a full audit, but for a first-pass check on a homepage or key landing page, it returns a useful snapshot in seconds without requiring an account. The SEO section covers meta tags, page titles, and basic indexation signals. If you are new to SEO health checks and want to understand the concept before committing to a paid tool, HubSpot's grader is a practical first step. Learn more about HubSpot's broader marketing toolkit at HubSpot.

Free SEO health check options

Paid platforms offer more pages, more depth, and better historical tracking, but several free options are good enough to find the highest-impact issues on a small site without spending anything.

Google Search Console covers everything Google itself has flagged, including index errors, Core Web Vitals failures, mobile usability issues, and manual penalties. It is the single most authoritative free source for SEO health data on your own site, and there is no reason not to have it set up on every site you manage.

Ahrefs Webmaster Tools gives free access to Ahrefs' site audit for verified site owners. It crawls your site and returns a health score alongside categorised errors, and it includes Ahrefs' backlink data for your own domain at no cost. For a site that cannot justify a paid Ahrefs subscription, Ahrefs Webmaster Tools is the strongest free technical audit available.

Google PageSpeed Insights is free and gives you both lab data and real-world Core Web Vitals data for any URL. It is the standard reference point for page speed performance and is the tool most closely aligned with what Google measures when evaluating page experience.

Screaming Frog SEO Spider in its free tier crawls up to 500 URLs and returns detailed crawl data including status codes, title tags, meta descriptions, H1 tags, canonicals, and image alt text. For sites under 500 pages, the free tier covers a full technical crawl without limitation. It does not provide a site health score, but the raw data it returns is more granular than most paid tools' summary reports.

Common SEO health issues and how to fix them

Most sites audited for the first time share a recognisable set of problems. Understanding what each issue means and how to fix it is the difference between an audit that produces a document and one that produces measurable improvement.

Broken links (404 errors)

A 404 error occurs when a URL is requested but no page exists at that address. Internal 404s waste crawl budget and leave users stranded. External 404s lose the link equity passed by the linking domain. Fix internal broken links by updating the anchor URL to point to the correct live page. Fix external ones by adding a 301 redirect from the old URL to the most relevant current page on your site.

Duplicate content

Duplicate content occurs when the same or substantially similar content appears at more than one URL. Common causes include URL parameters, HTTP vs HTTPS versions of the same page, www vs non-www versions, and trailing slash variants. Fix with canonical tags that point to the definitive URL, and ensure your server redirects all non-canonical versions to the correct one. If you are managing a site with an ongoing technical SEO programme, duplicate content is one of the issues that tends to recur without regular monitoring.

Missing or duplicate meta titles

Pages without a meta title get a default title generated from the page URL or the CMS template, which is rarely keyword-rich or click-worthy. Pages with duplicate titles compete against each other in Google's results. Write a unique, keyword-led title for every important page, 50 to 60 characters long.

Slow page load times

Page speed is a confirmed ranking signal on mobile. Slow pages also increase bounce rate because visitors leave before the content loads. The most common causes are uncompressed images, render-blocking JavaScript, and servers without caching. Use PageSpeed Insights to identify the specific opportunities on each page and tackle the ones with the highest estimated impact first.

Missing alt text on images

Alt text is the text description applied to an image via its alt attribute. It helps visually impaired users, and it helps Google understand what an image shows. Pages with many images and no alt text have a systematic on-page gap. Write concise, descriptive alt text for every content image. Skip decorative images or mark them with an empty alt attribute so screen readers skip them.

Thin content pages

Thin content pages provide little informational value to the visitor and are unlikely to rank for meaningful queries. Identify them by filtering your crawl for pages under 300 words. For each one, decide whether to expand the content to make it genuinely useful, merge it with a related page via a 301 redirect, or noindex it so it does not dilute your site's overall quality signal.

Crawl budget waste

Crawl budget is the number of pages Google will crawl on your site within a given period. Sites that waste it on paginated archive pages, URL parameter variants, or low-value admin URLs leave their important content under-crawled. Block unnecessary URLs in robots.txt and ensure your sitemap contains only the pages you want indexed.

SEO health checks by platform

The specific issues you will find in an audit depend partly on the platform your site runs on. Different CMSs create different default patterns, and knowing which issues are common on your platform saves time during the audit.

WordPress

WordPress is the most widely audited platform. Common issues include duplicate content created by tag and category archive pages, plugin-generated URLs that add URL parameters and create crawl waste, oversized image uploads without compression, and missing or poorly configured XML sitemaps. Rank Math or Yoast SEO handles on-page signals well, but neither solves server-level issues such as slow hosting response times. If your WordPress site runs on shared hosting, upgrading to a host such as Bluehost or Hostinger is often the single fix that makes the biggest measurable difference to page speed scores.

Webflow

Webflow generates clean, semantic HTML by default, which means many of the template-level issues common on WordPress are absent. The main technical SEO risks on Webflow sites are misconfigured canonical settings, pages accidentally set to noindex in the page settings panel, and collection pages that inherit thin content from short CMS entries. Webflow also does not have a native sitemap management feature as granular as WordPress plugins, so auditing the generated sitemap for excluded or duplicated URLs is worth doing after any major structural change.

WIX

WIX has improved its SEO capabilities substantially and now generates clean page titles, meta descriptions, and sitemaps from its built-in SEO settings panel. Common audit findings on WIX sites include pages with default or auto-generated meta titles, app pages that are not indexable, and JavaScript rendering delays that affect crawl speed. WIX's own SEO Wiz provides a basic health check integrated into the dashboard, though it does not replace a full crawl-based audit.

Shopify

Shopify creates duplicate content by default through its URL structure. Product pages appear at both /products/[handle] and /collections/[collection]/products/[handle], with the latter canonicalising to the former in most cases. Audit your canonical tags carefully on any Shopify site to confirm they are pointing to the correct canonical version. Shopify also does not allow editing of the robots.txt file on standard plans, which limits your control over what gets crawled. Running a Shopify-specific SEO audit with a tool like Semrush flags these structural issues alongside page-level on-page gaps. If your shop needs broader on-page support, there are strong options covered in the ecommerce SEO audit guide.

SEO health check reporting

An audit is only as useful as the action it drives. A report that lists 200 errors with no prioritisation leads to paralysis, not progress. The following approach turns raw audit data into a working plan.

Score and sort by severity

Most audit tools categorise issues as errors, warnings, and notices. Errors are the only category that reliably affects rankings and indexation. Work through errors first, then move to warnings. Notices are worth reviewing but rarely require urgent attention.

Group issues by fix type

Group your errors into categories: redirect issues, crawl issues, on-page issues, and page speed issues. Fixes within the same category often share a root cause or can be batch-resolved with a single change. For example, fixing a server configuration issue might resolve dozens of mixed-content warnings at once.

Assign ownership

Technical fixes belong to your developer or agency. On-page fixes belong to your content team. Redirect and hosting issues may sit with your platform provider. A useful audit report specifies who is responsible for each category, along with an estimate of the time required to fix it.

Track progress between audits

Set a baseline health score on your first audit, then rerun the crawl four weeks after the first round of fixes. Compare the before and after scores and document which categories improved. Tools like Notion or Airtable work well for tracking audit findings as a structured task list with status updates, so nothing falls through between audit cycles.

Include competitor benchmarking

A health score of 72 means more when you know your primary competitors score between 60 and 85. Ahrefs and Semrush both allow you to run site audits on competitor domains, giving you a direct comparison point. If your score is consistently higher than your competitors' but your rankings are not, the issue is likely backlink authority or content quality rather than technical health.

For a complete view of how your site stacks up against competitors on content and authority metrics, the SEO competitor analysis guide covers the full audit process in detail. And if you are combining a health check with a broader review of your link building strategy, the SEO audit tools guide compares the full suite of platforms available for ongoing monitoring.

Keeping records of each audit cycle is also practical for client reporting. Tools like Canva and Google Drive make it straightforward to turn audit data into visual reports that non-technical stakeholders can follow. If your audit process is part of a wider agency workflow, the guide to improving your SEO covers how to build a systematic optimisation programme that connects health check findings to traffic and ranking outcomes.

What this means for your site performance

A website SEO health check does not improve your rankings on its own. It identifies the specific barriers that are preventing your pages from performing as well as their content quality and backlink authority would otherwise allow. The value of the audit comes entirely from the fixes you apply afterwards.

Start with errors before warnings. Fix crawl and indexation issues before on-page issues. Run a second crawl after your first batch of fixes to confirm they resolved correctly and did not introduce new problems. Set a quarterly audit schedule and treat the health score trend as a KPI alongside your keyword rankings and organic traffic.

If you are checking your SEO score for the first time and want to understand what the individual metrics in your report mean, the guide on how to check your SEO score explains each component in detail. For sites where organic traffic is a primary acquisition channel, running a health check before a site redesign, a CMS migration, or a hosting change is one of the most cost-effective ways to protect the traffic you have already built.

The most common outcome from a first audit is a list of issues that were already affecting rankings without the site owner knowing. Technical errors accumulate quietly. A crawl surfaces them in one report and gives you a clear order of work. Sites that run audits regularly and fix issues systematically tend to see compounding improvements over time, not because any single fix was transformative, but because the clean technical foundation allows every other SEO effort to perform at its full potential.