Wetlands provide vital habitat for biodiversity and relevant ecosystem services to human population. The rapid transformation of freshwater wetlands to grow food crops became the wetlands strongly threatened by human activities. Restoration efforts related to wetlands have been widely attempted; however, science-based guidelines are relatively scarce. Here, we analyzed whether different levels of topsoil addition from natural wetlands in the sediment from rice fields influence the zooplankton communities. Our hypothesis was that the richness and abundance of hatchlings would be higher in treatments with high topsoil addition from natural wetlands, followed by treatments with low addition. In the laboratory, eight field sediment samples were incubated for zooplankton hatching in four treatments: rice fields, rice fields added with low (5%) and medium (30%) quantities of sediment from natural wetlands, and natural wetlands. A total of 4,493 hatchlings belonging to 24 taxa were observed in the experiment. While zooplankton richness and abundance did not differ between sediment treatments, significant differences in species composition associated with topsoil addition were observed. SIMPER analysis showed that topsoil addition from natural wetlands enhanced the abundance of cladocerans and larval copepods. Our results showed that sediments from natural wetlands have a bank of zooplankton dormant eggs that can help the recovery of wetlands disturbed by rice fields. The addition of natural wetland sediments in areas disturbed by rice fields modifies the zooplankton composition of the rice fields, aiding the recovery of disturbed natural wetlands for rice production.