This study investigates the determination of compound risk under the co-existence of heavy rainfall and water level rise at Alappuzha, a coastal district in Southern Kerala, India using Copulas. In the case of Alappuzha, when the combined action of rainfall and water level rise occurs, the chances of compound flooding is more in and around Vembanad Lake and lower Kuttanad regions. So, the water level and rainfall of three different locations viz. Punnmada, Cherthala, Arookutty are considered for compound flood risk analysis. A joint probability model based on Copula is used to determine the combined risk of flooding. First the marginal distributions of daily rainfall and water level data are developed for each locations and the best fit distribution is used for finding the joint probability. The three most common Archimedean copulas Gumbel–Hougaard (GH), Clayton and Frank are used to find the joint probability of rainfall and water level and the best copula for each location is also identified. Subsequently, the joint and conditional return periods of rainfall and water level are also obtained in an exercise of risk modeling. By using the digital elevation model (DEM) in a Geographic Information System (GIS) platform, the flood prone areas are calculated and represented them graphically, for specific cases of joint return period-water level combinations. This helps as an aid for administrators or policy makers to effectively perform the disaster management at Alappuzha.