Tainan, located in southwestern Taiwan, is a high-risk region for flooding and climate change effect and has a potential for future heavy rains. Groundwater pumping for aquaculture and irrigation along the coastal plain of Tainan is monitored due to subsidence. Predicting future subsidence and understanding the effect of climate change on subsidence can assist with regard to the planning and management of water and land resources in the early stages of subsidence, whose possible damage can thus be avoided. This study combines a physical model, called the nonlinear poroelastic model, and a gray-box model, called the gray system model, to evaluate and predict subsidence in the Tainan area. The subsidence under the climate change effect caused by changes in groundwater use is estimated. The climate change impact on subsidence and the potential for subsidence hazards are also analyzed. When taking into consideration the climate change effect, it is predicted that subsidence in Tainan will increase with increasing groundwater use. The maximum subsidence will increase from 29 cm (without additional discharge) to 34 cm (with additional 23.6 % discharge) and 35 cm (with additional 31.7 % discharge) in Xiaying District by 2039. The pattern of subsidence areas obtained by combining the nonlinear poroelastic and the gray system models is similar to that obtained using only the gray system model. However, the largest subsidence areas are different, and the subsidence quantity is much lower for the former due to the constraint of the physics-based poroelastic model. The combination of the nonlinear poroelastic model and the gray system model gives more reasonable estimations than either model can give alone. Large subsidence impact areas are located in the northwestern part of Tainan, and the largest impact is in Xiaying District. The potential for subsidence hazards is classified from the subsidence rates. The subsidence rate in Tainan is below 3 cm/year in the target years, and thus the potential for subsidence hazards is at middle and low levels. With climate change, the area with a middle level of potential for subsidence hazards extends across Yanshui, Xiaying, and Beimen Districts. From the study results, although the subsidence quantity is relatively low, rising sea levels and other effects of climate change expose Tainan to a high risk of flooding. Land and water resources should thus be managed to alleviate subsidence problems in the future.