The study was carried out in concrete ponds of the same rating (3.50 m×7.15 m×1.20 m) with the culture densities of 300 ind/m3 under the condition of no medicine and water exchange, the water levels were 40, 80 and 110 cm, respectively. The effect of different water levels(volumes) on nitrogen and phosphorus budgets in culture systems and the growth of Litopenaeus vannamei were analysed by 81 d period of freshwater indoor culture. The results showed that the survival and the per volume yield in the lowest water level (40 cm) group was significantly higher than those in the other groups (P<0.05). The feed coefficient in highest water level (110 cm) was significantly higher than that in the other groups(P<0.05). The length and weight of harvested shrimps showed no significant differences among three groups (P>0.05). The per unit yield showed significant differences among the three groups (P<0.05). The results also showed that feed was the main source of nitrogen and phosphorus inputs in each group, respectively accounting for 95.9%, 95.8% and 96.3% input of nitrogen and 97.5%, 97.5% and 97.8% input of phosphorus in ponds with water level of 40, 80 and 110 cm, respectively. 37.6%, 35.7% and 28.7% of nitrogen input and 12.6%, 14.0% and 11.5% of phosphorus input respectively in ponds with each water level were recovered as harvested shrimp biomass while 41.8%, 56.3% and 63.6% of nitrogen input and 77.1%, 66.4%, 73.2% of phosphorus input respectively in ponds with each water level remained in the water and sediment.