To make a system architecture diagram for web application, you can use a number of tools like Microsoft Visio, Lucidchart, or draw.io. Start by identifying the different components of your web application, such as servers, databases, APIs, and user interfaces. Then, create a visual representation of how these components interact with each other, including the flow of data and the communication protocols used. Be sure to label each component and include all details, such as programming languages or security measures.