Webmaster Tools is not updated in real time lie GA.

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Several members of the SEO community have called the Search Analytics report in Google Search Console (formerly Google Webmaster Tools) inaccurate, largely because the count of clicks does not match the count of sessions in Google Analytics for the source Google and medium organic.

Rather than inaccurate it’s really just a matter of trying to compare two completely different things. This article aims to cover how both are measured and a number of additional potential differences that need to be adjusted for when comparing these reports.

Clicks – Count of clicks from a Google search results page that landed the user on your property.

Sessions – Visits initiated by a user, counted when an HTML page loads the Google Analytics JavaScript snippet, adjusted for session timeouts.

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