Submerged macrophytes can improve water quality and buffer the effects of external nutrient loading, which helps to maintain a clear-water state in shallow lakes. We constructed 12 large enclosures with contrasting coverages (treatments) of submerged macrophytes (SMC) to elucidate their buffering capacity and resilience to nutrient pulses. We found that aquatic ecosystems with high SMC had higher buffering capacity and resilience, vice versa, i. e, the enclosures with high SMC quickly buffered the nutrient pulse and rebounded to clear-water state after a short stay in turbid-water state dominated by algae, while the treatments with low SMC could not fully buffer the pulse and rebound to clear-water state, and they slowly entered the transitional state after staying in turbid-water state. This means that the enclosures with high SMC had a better water quality than those with low SMC, i.e., the levels of nutrients and Chl-a were lower in the treatments with high plant coverage. In addition, plant coverage had a significantly positive buffering effect against nitrogen and phosphorus pulses, i.e., the nutrient concentrations in the treatments with high SMC took shorter time to return to the pre-pulse level. Overall, our results evidenced that the higher that the SMCs is, the better is the water quality and buffering capacity against nutrient pulses, i.e. the more stable is the clear-water state. However, low SMC may not be able to resist the impact of such strong nutrient pulse. Our results provide reference and guidance for water pollution control and water ecological restoration.