The Epidemic Prognosis Incorporating Disease and Environmental Monitoring for Integrated Assessment (EPIDEMIA) software system was designed and implemented to integrate disease surveillance with environmental monitoring in support of operational malaria forecasting in the Amhara region of Ethiopia [1]. The EPIDEMIA system consists of a collection of independent software subsystems, which were developed separately and are operating in different environments. The users who generate the weekly malaria forecasts are required to have considerable knowledge of the subsystems and manually perform a sequence of steps on these subsystems. As a result, the lack of top-level integration of the system became a barrier for the users to use the system effectively and transfer the technology. Research has been done on solving the barrier by integrating the EPIDEMIA system at the top-level with a simple interface. The result integrated system has a lightweight and user-friendly user interface that significantly reduces the time and effort for generating the forecasting reports and updating the visualizations. This paper briefly reviews the major subsystems of EPIDEMIA and the workflow steps involved in operating the subsystems. It focuses on presenting the details of the design and implementation of the integration.