Submerged macrophytes play a key role in the restoration of shallow eutrophic lakes. However, in some subtropical lakes, benthivorous fishes dominate the fish assemblages and influence the growth of submerged plants. A comprehensive understanding of the direct and indirect effects of benthivorous fishes on submerged plants is important. We conducted mesocosm experiments to examine the effects of three densities of benthivorous fish, Misgurnus anguillicaudatus, on the water properties, the growth, asexual reproduction, and the germination of turions of Potamogeton crispus L. Our results showed that fish disturbance increased TN, TP, PO4–P, NH4–N, and NO3–N of the water, raising the extinction coefficient K, Chl a, and the periphyton biomass. Benthivorous fish disturbance reduced the total biomass, root length, relative growth rate (RGR), and branching number while increasing the plant height of P. crispus. The P stoichiometric homeostasis coefficient (HP) (except turions) and HN was lower in plant tissues due to fish disturbance. Benthivorous fish disturbances promoted turions formation (e.g., increased turions total numbers and biomass) of P. crispus. Moreover, P. crispus exhibited transgenerational plasticity for benthivorous fish affecting turion emergence. The maximum final germination rate occurred only when fish density in the mother plant grow experiment matched that in the turion germination experiment. Turions generated by P. crispus disturbed by low‐density fish exhibited increased germination rates. Our findings suggest that controlling benthivorous fish reduces its indirect and direct effects on submerged vegetation, facilitating the successful restoration of these plants.