Understanding Indexing Challenges for Large-Scale Taxonomy Websites: Strategies for Managing Extensive URL Portfolios

In the realm of large-scale, taxonomy-driven websites, maintaining effective search engine visibility can pose unique challenges. Recently, many site operators have observed changes in how Google indexes sprawling collections of deeply nested pages. This article explores common experiences, potential causes, and strategic considerations for managing extensive URL structures, drawing insights from a representative case study.

Case Overview

Consider a sizable website cataloging approximately 350,000 insect species, structured hierarchically as follows:

  • Family > Subfamily > Species > Photos/Maps > Individual Data Pages

This site primarily features static content in Spanish, updated annually to reflect new discoveries or data.

Observations in Search Console

The site owner reports significant indexing concerns:

  • 143,000 URLs are marked as “Crawled – currently not indexed” — predominantly lower-level pages such as photos, maps, and data pages.
  • 68,000 URLs are “Discovered – currently not indexed” — mainly from those same lower tiers.

Notably, these issues have emerged since 2022, coinciding with Google’s helpful content updates and core algorithm modifications. Historically, this site’s pages indexed effectively, but recent shifts have led to reduced visibility for bulk, detailed subpages.

Discussion and Considerations

  1. Is this behavior typical for large, structured sites?

It is increasingly common for major websites with extensive hierarchies and deep linking structures to experience decreased indexing of lower-level pages, especially if those pages offer less unique or substantial content. Google’s algorithms prioritize high-quality, valuable pages, which can sometimes result in deep or less distinctive pages being excluded from indexing.

  1. Could the abundance of non-indexed URLs impact overall site performance?

Excessive non-indexed individual pages may generate crawling overhead or dilute crawl budget, potentially affecting critical pages higher in the site hierarchy. However, if these pages are low-value or duplicate in essence, this may be a natural filtering process rather than a detrimental issue.

  1. Should the site consolidate or merge lower-level pages?

Consolidation strategies may include integrating photos, maps, and data into broader species pages, reducing URL complexity. This approach can:

  • Simplify the site architecture
  • Enhance content depth on principal pages
  • Potentially improve indexation and ranking signals

But caution is advised: such consolidation should ensure that valuable user experience and SEO signals are maintained.

Strategic Recommendations

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