The development of information technology today has had a significant impact on the use of websites in various sectors including the military. In addition to facilitating the optimal dissemination of information, the use of websites can cause information security problems related to Confidentiality, Integrity, and Availability. Indonesian Navy perimeter data shows Indonesian Navy sites faced 2,720,027 significant attacks. In the period February 2022 to September 2023, 290 cases of defacement attacks were found on Indonesian Navy websites related to online gambling using the Google dorking method. The aim of this research is to propose the use of an open sourcebased Web Application Firewall (WAF), especially ModSecurity which is integrated with Yara Rules to complement system security and become an alternative to the existing WAF (Imperva). This research method is a quantitative experimental method used to compare the performance of the developed WAF with the existing WAF. The results of research testing using ModSecurity on WAF Imperva with SQL injection attacks show that the test resulted in detection of 90.84% and an increase of 0.16%, while XSS attacks were able to prevent 99.94% with an increase in detection of 2.40%. Other test results on Malware attacks show that the ModSecurity integration test results with Yara Rules on WAF Imperva can provide malware detection and prevention of 90.88%, this shows an increase of 0.04%. It is hoped that this research can be an alternative solution in handling the Indonesian Navy's security system infrastructure.