The physiological responses of scallop Chlamys farreri to changing environmental conditions were researched in semi-field water-flowing system, based on a recently developed biodeposition method. There was no significant relationship between clearance rate and stocking density or food concentration. The absorption efficiency of the scallops was not markedly affected by the stocking density and the POM. The mean POM absorption efficiency was 75.9% and relatively high, which could be attributed to low food concentration. The energy loss by excretion of amino acid was higher than that by the excretion of ammonia. The gross ecological efficiency of N (mean value 9.9%) was higher than that of C (mean value 5.9%) or P (mean value 4.1%). In the nitrogen budget, if only NH4(+)-N was considered and other forms of nitrogen such as amino acids were neglected, a significant error (a mean about of 20%) could arise. It was suggested that whether in energy or element budget, the shell should not be neglected. In coastal intensive raft-culture areas, scallops might give great impact on energy flow and cyclings of matter and nutrient by filtration, respiration, excretion, egestion (biodeposition production) and growth.