Overapplication of manure in sensitive watersheds is an issue of increasing environmental concern due to increased nutrient loading and antibiotic release into aquatic environments. Manure is typically surface applied, leaving nutrients and antibiotics vulnerable to loss at the soil surface. Elevated nutrient and antibiotic loading into water bodies can increase the rate of eutrophication and occurrence of antibiotic resistance genes in areas of high animal agriculture production, such as the Chesapeake Bay watershed. Manure injection is a new technology that incorporates manure into the soil with minimal disturbance, and management strategies that reduce manure loss from agricultural fields could prevent the transport of nutrients and antibiotics to sensitive waterways. However, little is known about the efficacy of dry litter injection to decrease nitrogen (N) loss when compared to surface application. Also, there are no studies that determine the effects of injection on antibiotic transport and transformation after manure application. Therefore, this project focused on changes in N cycling, orchardgrass hay yield and quality, and transport and transformation of pirlimycin and cephapirin, two common antibiotics in dairy production, when manure is injected. Subsurface injection eliminated ammonia volatilization and N loss in runoff and increased soil inorganic N when compared to surface application after volatilization, incubation, and rainfall simulation studies. Although these benefits did not translate to higher yields in orchardgrass hay, protein increased when poultry litter was injected, indicating greater N uptake. Injection of dairy manure decreased losses of pirlimycin to levels of the control when compared to surface application. Although, pirlimycin had a slower degradation rate within the injection slit compared to surface application, potentially increasing the amount of time soil microbes are exposed to antibiotics. In an incubation study, pirlimycin concentrations decreased after 7 days, but concentrations increased sharply after 14 days. This indicates that conjugates formed in the liver or digestive tract of dairy cows may revert back to the parent compound after manure application. With increased retention of nutrients and antibiotics, injection could be a best management practice used to reduce the loss of these compounds to the environment while increasing the quality of crops produced.