The hydrochemical features affected by differing land uses play a key role in regulating both the primary production of aquatic photosynthetic organisms and the formation of autochthonous organic carbon (AOC); this impacts eutrophication and the global carbon cycle. In shallow water environments where phytoplankton and submerged plants coexist, the C-N-P limitations on the primary production of these aquatic organisms, and the mechanisms by which they promote the formation of AOC are poorly understood. In this study, over the hydrological year September 2018 to August 2019, a large-scale field simulation experiment at the Shawan Karst Test Site (SW China) with various types of land use was systematically conducted to investigate the C-N-P limitations on the primary production of phytoplankton and submerged plants. The results indicate that (1) phytoplankton are co-limited by nitrogen (N) and phosphorus (P) but with the N more important, while submerged plants are limited by carbon (C); (2) Chlorophyta and Bacillariophyta display a stronger competitive advantage than Cyanophyta in aqueous environments with high C but low N-P; (3) there is a seasonal difference in the contribution of phytoplankton and submerged plants to the formation of AOC, however, throughout the year, the contributions of phytoplankton (27%) and submerged plants biomass (28%) to AOC concentrations in the water were similar, combinedly accounting for approximately 17% of the formed AOC. It is concluded that natural restoration of vegetation, or injecting CO₂ into water, which results in higher C but lower N-P loadings, may simultaneously help to mitigate eutrophication (with changes in biological structure and species) and increase C sequestration in surface waters.