Search engines have crawled and indexed hundreds of billions of pages on the web, but this is just a fraction of the true size of the content available.
Search engines browse the web looking for pages. They look for links and follow these links, always on the hunt for pages to index and they are very good at this. They are not very good at finding pages with no links to them though. They can not perform searches on websites they way we would, and so have no access to content that is generated on the fly by a search or form that a human would use.
The deep web is the content that search engines do not have access too.