A covered anaerobic lagoon system for swine manure management has been evaluated for its performance. The system consists of a covered anaerobic lagoon for primary treatment and a conventional lagoon for water storage. TP, OP, COD, TOC, TS, and VS were reduced by 74, 58, 94, 93, 75, and 87% respectively in the covered anaerobic lagoon, and by 62, 58, 28, 18, 23, and 27% respectively in the storage lagoon when the pits were discharged every eight days. TKN and NH3-N were reduced by 80% and 84% respectively in the storage lagoon. When the pit discharge frequency was changed to four days, no significant different was observed for the removal efficiencies. Methane production was affected by the temperature in the covered lagoon and the pit discharge frequency. Significant pathogen and odor reduction was observed in the system.