Groundwater is a critical and strategic water resource, and its scientific development, utilization, and protection are related with the collaborative healthy development of human society and ecosystems. Therefore, groundwater has always been one of a hotpot and focus in natural science. This paper presents a statistical analysis of the funding of groundwater science from National Natural Science Foundation of China during 1986 to 2022. The current status of groundwater scientific research is summarized based on the discipline distribution, project types and primary research directions of funded projects. Current gaps and bottlenecks are revealed, and the development trend of groundwater science is assessed. The study results indicate that first of all, the number and types of funded projects in the field of groundwater science are increasing rapidly. Secondly, groundwater science is intersected closely with other disciplines via more and more frequency, representing a “multi-point flower” in the application and funding projects. Thirdly, groundwater science, as a branch of Earth science, is facing new opportunities and challenges. Many major scientific issues need to be addressed urgently, so further efforts are needed to enlarge the financial support to major projects. Fourthly, groundwater science research has the potential to intersect with more related fields, such as oceanography, chemistry, meteorology, and atmospheric science. The National Natural Science Foundation of China can serve as a cultivation platform for the intersection of groundwater science and other disciplines.