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Web applications have become exponentially popular and significant in our daily life with the growth of Internet. At the same time, there is an increase in number of attacks on web applications targeted by hackers and cyber crooks. Attacks like injection vulnerabilities such as SQL Injection, Cross site Scripting, Cross site Request Forgery(CSRF) are common and caused due to inputs performed by a user which are not properly validated across the web applications. This paper specially focuses on input based attacks and their mitigation. Here, we have implemented various attacks on a Giftshop web application and also classified their countermeasures with respect to Software Development Life Cycle. Finally, the result of vulnerability scanners are shown and analyzed before and after the implementation of the countermeasures.