Submarine groundwater discharge (SGD), a major component of the hydrological cycle, has significant impacts on the sustainable development of the marine environment. This study aimed to examine the literature characteristics and research hotspots of SGD based on Web of Science’s citation database from 1998–2019. With systematic bibliometric analysis, insights were made into multiple aspects including research output, subject categories, journals, countries/territories, institutions, authors, and hotspots and research trends. Results showed that the current amount of publications on SGD has increased exponentially. The characteristics of multi-subject, active international and inter-institutional collaborations were identified. There were 11 core journals publishing the research on SGD, and the number of covered journals increased linearly from 1998. USA had distinct advantages in publication outputs and took the core position in international collaborations. At present, the research hotspots of SGD mainly include the following: dynamics process and estimation of SGD with hydrogeological methods, tracer techniques, geochemical process in subterranean estuary, and dissolved material inputs to coastal waters via SGD. Citation analysis implied much development space in carbon flux transported by SGD and the implement of head as groundwater tracer. These results provided an instructive perspective of the present situation and future research direction on SGD.