The excessive proliferation of filamentous green algae has been identified as a key factor affecting the growth and community stability of submerged macrophytes in a clear water, macrophyte-dominated shallow lake. Macrobrachium nipponense grazes on filamentous green algae, but its presence can increase water nutrient levels if it disturbs the sediment. However, the effects of M. nipponense on lakes in the early stages of restoration remain unknown, particularly its impact on filamentous green algae. To address this knowledge gap, a composite system comprising two submerged macrophytes (Vallisneria denseserrulata and Hydrilla verticillata) and filamentous green algae treatments was established in late spring and early summer. This system was utilised to investigate the influence of M. nipponense on the proliferation of filamentous green algae (Spirogyra sp. and Cladophora sp.) and the associated environmental factors. The results obtained demonstrate that M. nipponense exerts a significant effect on the reduction of Spirogyra and Cladophora cover and biomass. Furthermore, M. nipponense has been shown to reduce phytoplankton and epiphyton biomass, as well as total nitrogen and total phosphorus concentrations. Although the growth type of submerged macrophytes did not have a significant effect on Spirogyra or Cladophora biomass, the presence of M. nipponense led to a greater reduction in Spirogyra cover than Cladophora cover. Furthermore, the presence of M. nipponense led to a decline in epiphyton biomass on the leaves of V. denseserrulata and H. verticillata. Significantly, the impact of M. nipponense on phytoplankton biomass and total nitrogen concentrations was more pronounced in Spirogyra treatment compared to the Cladophora treatment. In the absence of shrimp, no substantial disparities were observed between the two treatments. These findings suggest that the introduction of M. nipponense into shallow lakes during the late spring and early summer months can lead to a decline in filamentous green algal biomass and nutrient concentrations, thereby enhancing water quality. However, the responses of clear water systems with submerged macrophytes and various filamentous green algae to the introduction of M. nipponense vary.