Soil erosion in Southeastern China covers an area amounts to 21.4% of the total. At watershed scale, the GIS coupling model is an effective approach to assess agricultural non-point pollution and best management practices. In this study, the SWAT (Soil and Water Assessment Tool) was used to simulate the transfer of water and nutrients in the Lianshui basin in Southeast China from 1991 to 2004. The basin has an area of 579 km², an annual mean temperature of 18.9°C and rainfall of 1500 mm. The main objective is to: 1) reveal the climate effect on water and nutrient loading; 2) increase the applicability and accuracy of SWAT. The Lianshui basin was divided into 62 sub-basins using the Digital Elevation Model, then the sub-basins were further divided into hydrological response units with a uniform soil and land-cover type. Land-cover map was derived from visual interpretation of Landsat TM images. Soil information was obtained by field investigation based on geostatistical sampling and analysis. Water and sediment monitoring has been conducted since 1954 and nutrients (N and P) loss monitoring since 2002 at the outlet of basin. The hydrological simulation was validated by comparing the stream flow measured with that calibrated by digital filter program which partitions the stream flow into base flow and surface runoff. The measured annual water flow changed from 739 to 1816 mm, and and sediment yield from 271 to 817 ton/km². The monthly transfer of N changed from 239 to 3298 kg/km². The Nash-Sutcliffe coefficient for the simulations of annual flow, annual sediment yield, monthly flow and monthly sediment yield over 1991 to 2004 were 0.91, 0.76, 0.83 and 0.68, respectively. In a monthly step, the Nash-Sutcliffe coefficient for the simulations of total nitrogen and total phosphorus loss over 2002 to 2004 were -0.15 and -0.12, respectively.