A mathematical model is used to investigate nitrogen dynamics in the intensive aquaculture ponds in the western coast of Korea. Parameters associated with water quality, sediments and growing of shrimp (Fenneropenaeus chinensis) are measured to calibrate the model for feeding ponds A and B and storage ponds. The model describes the fate of nitrogen including loadings of ammonia from feeds, phytoplankton assimilation, nitrification, sedimentation, volatilization and discharge. The model obtains good agreements with the measured values of TAN $(NH_4,;NH_3),;NO(NO_2,;NO_3)$ and Chl (chlorophyll a). Impacts of water exchange on TAN and Chl are investigated, showing that the range of 0.01-0.2 (/day) cannot effectively reduce TAN but reduces Chl. Nitrogen in the ponds A is removed by sedimentation $66\%,$ volatilization $8\%,$ discharge of particulate and dissolved $8\%.$ The pond B shows $56\%;and;26\%$ of sedimentation and volatilization, respectively, to yield $10\%.$ decrease and 8c/o increase compared to those in the pond A. While the pond A has larger area (1.02:0.66 ha) and same stocking density (0.025 md./L) at the beginning of culture, the pond B obtains higher stocking density (0.0065:0.0091 md./L), longer feeding period (103:121 day) and resultant higher shrimp production (1.15:2.13 t/ha/cycle) at harvest. This is possibly due to the hydraulic characteristics driven by paddlewheels. At low ratio of the low speed area and the pond area, the rate of sedimentation is high, while the rate of gas exchange is low. Thus, the measurement and model analysis suggest that water quality and shrimp production are positively correlated with the hydraulic characteristics in the shrimp ponds.