There's a reason most websites use a top navigation bar. On a website, content is king, so you need as much width space as possible to display everything. But for web applications, navigation is king.
Users aren't trying to explore content but rather complete tasks efficiently. If your app doesn't have optimal navigation, users won't be satisfied using it. Doing tasks will take more time and effort than normal.
The key to a satisfying web app navigation is placing items at expected locations. Doing this will make them faster to find and easier to remember (source). The end result is a navigation shell that looks like this.