Contaminant reduction through sustainable agricultural practices is critical for maintaining human, livestock, and environmental health. Our research sought to contribute to a holistic view of phosphorus and antibiotics as contaminants in agriculture. The hydrologic flow paths that transport these contaminants from manure connect agricultural systems with surface waters and drinking water supplies. These compounds are concerning due to their influence on soil and aquatic ecosystems and, subsequently, human and livestock heath. To understand transport of these compounds, we designed field scale, laboratory scale, and interview-based studies. We assessed the effectiveness of a cattle exclusion riparian buffer in reducing total and soluble reactive phosphorus loads (Chapter 1), and found the practice reduced stream phosphorus, but may be more effective when implemented adaptively around variable source areas. We determined adsorption characteristics of erythromycin (a macrolide antibiotic used on farms) to soil in the presence and absence of manure (Chapter 2) and found that the antibiotic is more mobile in the presence of manure and sorbs more readily to soil in the absence of manure. Lastly, we interviewed central New York dairy farmers to understand farmer perceptions of transport pathways of antibiotics on dairy farms (Chapter 3) and found that there is a strong divide in perception of these compounds as contaminants between organic and conventional farmers, that farm size and farmer age influence perceptions and management decisions around treatment and transport, and that contamination of market products was a higher concern than environmental contamination. The scales and methods applied in this work combine to provide a broader perspective with which to guide future contaminant mitigation efforts.