The effects of submerged plant-induced calcium and phosphorus coprecipitation on the phosphorus cycle in aquatic environments and interspecific differences are still unclear. Herein, we selected Ceratophyllum demersum L. and Potamogeton crispus L. to construct a sediment–water-submerged plant system. We examined how phosphorus concentrations in the water, sediment, and plant ash changed over time with different phosphorus and calcium treatments and explored the effects of photosynthesis-induced calcium and phosphorus coprecipitation on water’s phosphorus cycle and variations between different submerged plant species. The main results were as follows: (1) The phosphorus reduction in the P. crispus system was less than that in the C. demersum system. (2) P. crispus had higher total ash phosphorus (TAP) values than C. demersum. (3) The sediment total phosphorus (STP) and its fractions with P. crispus were most affected by phosphorus concentration while those with C. demersum were most affected by time. Overall, the two submerged species exhibited different calcium and phosphorus coprecipitation levels and had distinct effects on the water-to-phosphorus cycle. When submerged plants are introduced to reduce and stabilize the phosphorus levels, plant interspecific differences in their induced calcium and phosphorus coprecipitation on water and phosphorus cycling must be fully assessed.