Site specific farming systems have the potential to increase farmers' net income by reducing the use of agro-chemicals and applying variable rate technology for areas showing stable yield patterns. This study was designed to: (1) study yield patterns in given fields using variography; (2) seek correlation among soil attributes and yield data using GIS; and (3) simulate the effects of N-fertilizer and swine manure application rates on NO 3-N losses with subsurface drainage water and crop yields. The results of this study showed that the spatial correlation lengths were found to vary from 40 m for corn to about 90 m for soybean. The lack of temporal stability in either the large-scale deterministic structure or small-scale stochastic structure revealed that yield variability was not only controlled by intrinsic soil properties but also by other extrinsic factors including climate and management. Map overlay analysis showed that areas of lower yield in the vicinity of Ottosen and Okoboji soils for corn in a central Iowa field were consistent from year to year whereas areas of higher yield were variable. Results from both GIS and statistical analysis showed that interactions between soil type and topography has a more pronounced effect on yield variability patterns for this field;The simulation component of the study showed that the Root Zone Water Quality Model (RZWQM, V. 3.25) predicted subsurface drain flow, NO3-N concentrations in subsurface drain water, NO3-N losses with subsurface drain water, and grain yields satisfactorily by showing an average difference of --10.9%, --7.2%, --5.6%, and 0.9% respectively, between predicted and observed values for all the N-fertilizer treatments for the years 1996 and 1998 for a central Iowa field. Model simulations for 1996 and 1998 showed that by doubling the N application, the grain yield increased on the average by 46% and NO3-N losses increased by 42%. By increasing the N applications four times, the grain yields increased by 55% and NO 3-N loss increased by 60%. These results showed that the increase in corn yield was not linearly proportional to the N applications. The calibration and evaluation of the RZWQM for the northeast Iowa fields indicate that RZWQM has the potential to successfully simulate the effect of N and manure management systems on corn yields and NO3-N concentrations in the subsurface drainage water.