With the increasing urbanization rate, higher demand is placed on drainage systems, necessitating analysis of their risk profiles. While many studies focus on the individual hydraulic modeling of stormwater and wastewater systems when considering operational risks, they often overlook the exacerbating effects of combined stormwater and wastewater flows on each other’s risks. In this study, we constructed a model of the combined stormwater and wastewater drainage system in Lijiao, Guangdong Province. We analyzed the operational risks of both stormwater and sewage networks in different scenarios, focusing on full-load pipes, overload pipes, node overflows, and minimum flow velocities. Furthermore, we compared the exacerbating effects of sewage and stormwater on each other’s network operational risks. Simulation results indicated that, for sewage networks with combined sewer sections, the lengths of full-load pipes and overload pipes increased by an average of 27.4% and 16.3%, respectively, during rainy weather scenarios compared to dry weather. After considering the inflow of sewage into combined sewer sections, the average length of full-load pipes increased by 3.8 km, overload pipe length increased by 1.1 km, and overflow volume increased by 2.26 × 104 m3. As the return period of rainfall events increases, these inter-system impacts gradually diminish. Therefore, when modeling drainage systems and assessing operational risks, particularly during low return period rainfall events, the inclusion of both stormwater and sewage in combined sewer networks should be comprehensively considered.