Common Issues with Internal Linking in SEO and How to Fix Them

Why internal linking matters for SEO

Internal links connect pages, pass link equity, and guide both users and search engines through your site’s funnel. Many growth teams focus on external backlinks and technical SEO but overlook structured internal linking, which directly affects ranking opportunities, crawl efficiency, and conversion paths. This guide covers the most common issues with internal linking in SEO and provides tactical fixes you can implement on Shopify, WordPress, or custom platforms used by US eCommerce and B2B sites.

Common problem 1: Orphan pages and hidden landing pages

Orphan pages are pages that have no internal links pointing to them. They are hard for crawlers to find and rarely rank. Orphan pages often happen when content is created for campaigns, microsites, or long-form resources but never integrated into the main navigation or topic clusters.

• Identify by running a site crawl (Screaming Frog, Sitebulb) and comparing the crawl to your sitemap.
• Solution: add contextual links from category pages, blog posts, or product collections and include them in your XML sitemap.

Common problem 2: Poor or generic anchor text

Using vague anchors like "click here" or repeating exact-match anchors across many pages wastes semantic signals. Anchor text helps search engines understand the target page topicality. For US product and service pages, optimize anchors to reflect user intent and the conversion stage (TOF → MOF → BOF).

Common problem 3: Excessive links and navigation bloat

Crawl budget is usually not a concern for most small and medium US sites, but a bloated header/footer with hundreds of links dilutes internal equity. Keep navigational links focused on user paths that lead to revenue or lead capture.

How to diagnose internal linking issues

Start with a data-driven crawl and analytics review. Use crawl tools to surface orphan pages, broken links, redirect chains, and excessive depth. Combine that with Google Search Console coverage and internal site search logs to understand which pages users and bots actually reach.

Quick diagnostic checklist

• Run a full site crawl and export internal link counts per URL.
• Compare indexed URLs in Google Search Console to your sitemap.
• Audit anchor text distribution for repetitive or generic phrases.
• Identify redirect chains and broken internal links (HTTP 4xx/5xx).
• Map pages to funnel stages (TOF, MOF, BOF) and confirm internal paths exist.

If you need a strategic reference for how performance-driven agencies build scalable linking systems, review Prebo Digital’s service approach. Our methodology pairs technical tracking with funnel-first optimization: Services overview. For an organizational view of our company and approach, see the agency profile at Prebo Digital.

Tactical fixes for the most common issues

Fix orphan pages and improve discoverability

Add 2-3 contextual links from high-authority internal pages that are relevant to the orphaned content. For product pages on Shopify stores, link from category collections and related product modules. For SaaS/B2B content, create a pillar page and link supporting resources into it.

Improve anchor text and topical signals

Use descriptive anchors that match user intent at each funnel stage. Example:

Resolve redirect chains and broken links

Redirect chains waste crawling resources and dilute equity. Replace chains with direct 301s to the final URL and fix broken 4xx links. Monitor this via server logs and periodic crawls.

Balance navigation vs. contextual linking

Use a tiered approach: primary navigation for high-value categories, secondary nav/collections for discovery, and contextual inline links for depth and relevance. Avoid stuffing the footer with every page - instead prioritise pages that drive revenue or lead generation.

Operational checklist and governance

Make internal linking a documented part of your content and product release workflow. Include a pre-publish checklist that covers canonical tags, XML sitemap updates, and at least two incoming internal links for new content. For teams scaling across product and marketing, consider a lightweight tagging system that ties pages to funnel stages and priority.

Example governance steps

• Content brief includes desired anchor text and two source pages for links.
• Engineering tickets that change URLs include an internal-link review to update upstream links.
• Monthly crawl report with action items: fix 404s, collapse redirect chains, add contextual links to underperforming pages.

If you want a practical example of linking strategies applied to a revenue-focused funnel, explore how teams align content and conversion in a structured growth framework by visiting our team page: About Prebo Digital. For collaboration on technical fixes and tracking, our contact page outlines engagement steps: Contact.

Measuring impact and next steps

Track improvements by measuring organic sessions, impressions, and conversions for affected pages over a 4-12 week window in the United States. Combine crawl metrics (internal link counts, depth) with GA4 behaviour reports and Search Console performance data. Expect incremental gains; internal linking improves discoverability and ranking potential but should be part of a broader CRO and technical SEO program.

Quick wins to prioritise this month

• Add internal links to three orphan or low-traffic pages that support revenue goals.
• Replace generic anchors with descriptive phrases aligned to funnel stage.
• Fix redirect chains longer than one redirect and patch 404s encountered by users.

Sources

• Google Search Central - Link best practices
• Ahrefs - Internal linking guide and case studies
• Moz - Why internal links matter for SEO