The demand for web applications increased exponentially in the mid-1990s. With the emergence of object oriented programming languages, distributed web applications were built with the former client-server model that simultaneously solved the purpose of many online applications. Since then, Java has become dominant in the world of enterprise application development. This dominance of Java language is due to open source frameworks and many third party communities. In recent years, Spring and Hibernate-ORM (Object Relational Mapping) are the two most influential and famous open source frameworks, which stood out and are contributing an enormous success in the development of web applications. This research will study the advantage of combining both Spring and Hibernate and, how it affects the performance, programmability, cross cutting concerns and portability of an enterprise web application. Along with that, this research will particularly focus on Spring MVC (model, view, control) -- an open-source web application framework, Spring AOP (Aspect Oriented Programming) for handling cross cutting concerns and analyze the advantages of using Hibernate over traditional JDBC (Java Database Connectivity) in Spring projects. To really understand how it is possible, a web application with layered architecture is built for managing computer science past thesis defense documents called TMS (Thesis Management System) using Hibernate and Spring frameworks.