The term website refers to a collection of interlinked web pages hosted on the internet, which can be accessed using a particular URL or Uniform Resource Locator. Web application, on the other hand, is a software application that can be accessed via a web browser, most times over a network, but can also be accessed even when it is not connected to a network.
Most times, a web application can be hosted as a separate page on a particular website, and it won't have anything to do with other resources on the website. While there are different kinds of web applications, they will first process the information stored on them from their databases.
To understand this better, common examples of web applications are spreadsheets, Gmail, Yahoo, word processors, file conversion software, etc. Depending on the nature of websites you are creating, some websites can still be created even with HTML code, while web applications are most times created with more advanced programming languages.