Nonpoint source pollution continuously draws the attention of both scientist and the public. Nutrient and microbial pathogens from the application of liquid swine manure (LSM) have been implicated as the source of contamination and pollution to water and soil. The overall goal of this dissertation was to investigate the effects of LSM on nutrient loss and pathogenic bacteria transport to subsurface drainage water quality under corn and soybean crop rotation. A field experiment at the plot-scale was conducted to achieve this goal. Data collected from the 6-year experiment (2001-2006) at Nashua research site was used to study the effects of LSM applied to both corn and soybeans in comparison to manure applied to the corn phase only in term of NO3-N and PO4-P losses to subsurface drainage and its residual in the soil. Data used for investigation of directly connected macropores in transporting bacteria from soil surface to subsurface drainage were conducted in four different experiments in 2008 and 2009. Overall the results showed that LSM applied to soybean crop every year increased the NO3-N in subsurface drainage water and accumulated a high concentration of phosphorus in soil profile, especially in the top 30 cm of soil depth. So, the changes of this LSM application should be modified in terms of application rate and/or adding a land cover crop to minimize the contamination of these nutrients. Also, transport of bacteria like E. coli from LSM through macropores, especially for the ones that are directly connected from soil surface to subsurface tile drainage are clearly shown. This is specially shown in the first three hours if rainfall occurred after manure application. For these reasons, it is suggested that weather conditions should be seriously taken into consideration in the timing of the LSM application in order to minimize the transportation not only of bacteria, but also nutrients to tile drainage.