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This research focuses on the efficiency of recommended heavy use area protection (HUAP) pads installed in poultry houses utilizing the Choptank River, a tributary of the Chesapeake Bay. The Chesapeake Bay watershed is severely affected by crop agriculture and poultry feeding operations. Water quality degradation along with scarcity of water is a significant concern in this area, suggesting a need for changes in both environmental and groundwater management practices. Our objective in this study was to compare the efficiency of HUAP in reducing litter spillage and nutrient runoff between two poultry houses, one of which was constructed in 2005 and the other in 2009. The poultry house constructed in 2005 did not have HUAP pads initially; they were built in 2006. The poultry house built in 2009 had the pads from the starting point. We collected soil and water samples each month and analyzed them for pH, electrical conductivity (EC), nitrate, nitrite, total nitrogen, phosphate, and other soil properties throughout the year. The pH of soil and water samples was in the range of 6.8–8.0 and 6.5–7.2, respectively. We collected six water samples in total in the ditch, from points at retention ponds near the farm ditch to sites in wooded areas on the farm. Water sample B (where ditch water meets retention pond water from the poultry farm) had the highest EC value and nitrate, nitrite, and total nitrogen concentrations compared with other water samples. The subsequent water samples downstream had reduced loads of nutrients. The study results suggest that there was a minimum carryover of nutrients from soil into the runoff water, storm ditches, and adjacent stream. There was also a minimal effect of house cleaning and storm events in raising the concentration of nutrients in soil and water samples at our study sites. The older poultry site had higher total nitrogen and phosphorous surrounding the pads, whereas no elevated levels of nutrients were identified at the newer site. The ability of HUAP pads to hold onto contaminates decreases with age and use. This study also shows that the impacts from poultry activities on surface and groundwater can be minimized by using management practices such as HUAP pads. These practices can reduce pollution in the farm, increase productivity, and save farmers and ranchers time and money in the long run.