The structure of a site indicates the "physical" arrangement and connection of pages. It doesn't, however, determine how pages and content is thematically related. A hierarchy—which you'll most likely be dealing with—is agnostic to the categories of pages that comprise the structure. Regardless, if the navigation is categorized by subject, by date, or by audience, the structure will still be hierarchical. In addition to determining the site structure, the next step in navigation design is to consider the types of categories and topics that will be used to organize information. But note that defining a structure and organizing categories of content go hand in hand. One may not precede the other.
The organization of a site's navigation itself can be instructional, potentially helping visitors better understand the topic at hand. Providing a logical categorization of options and grouping them by a consistent scheme increases the ease with which people can comprehend and use a navigation menu. This in turn adds to the predictability of navigational links, potentially bringing visitors closer to their ultimate goal.
The general recommendation for navigation design is to create menus that share a common organization. For instance, it might be confusing to see the following options within a single navigation mechanism:
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Instead, navigation design seeks to create menus out of a similar links. This ...