This study reports the primary production of phytoplankton determined with a 13C tracer, and their related variables, in Lake Kasumigaura, a shallow, hyper-eutrophic lake, and the second largest lake in Japan. Measurements were conducted monthly from August 1981 to December 2013 at four stations within the lake. Monitoring was a component of the Lake Kasumigaura Long-term Environmental Monitoring program, conducted by the National Institute for Environmental Studies (NIES) since 1977. The program collects data on water quality, and plankton and benthic communities. Lake Kasumigaura is registered as a core site of the Japan Long-term Ecological Research Network (JaLTER), which is a member of the International Long-term Ecological Research Network (ILTER). This dataset includes daily primary production Pzd: gC m-2 d-1) and the six parameters required to calculate Pzd: maximum photosynthesis rate (Pmax : gC gC-1 h-1); light irradiance at the junction of the initial slope (α: (gC gC-1 h-1)(μmol photon m-2 s-1)-1) and Pmax of the photosynthesis vs. irradiance (P vs. E) curve (Ek: μmol photon m-2 s-1); attenuation coefficient of photosynthetically available radiation (PAR) (KPAR: m-1); water depth at each sampling station (Zb, m); dissolved inorganic carbon (DIC: mgC L-1) and particulate organic carbon concentrations (POC: gC m-3); and chlorophyll a amounts (Chl.a: μg L-1). Daily primary production was calculated by obtaining a P vs. E curve over a short-term incubation (approximately 1 h) ina water tank using in situ water temperature in the laboratory, based on the field conditions of the sampling date. The dataset has been used for ecological studies as well as for management studies on water quality and ecosystems. This dataset is unique among the available published papers concerning lakes or primary production in various ecosystems, collected over a long period of time and freely available.