Anticoccidants, biochemically known as ionophores are added to poultry feed for growth promotion, prophylactic and therapeutic purposes to better sorb nutrients and against coccidiosis caused by parasite Eimeria sp. Ionophores belong to the class of emerging contaminants, as they are not regularly monitored in the environment and not specifically treated in the effluents. Potentially, this can cause ionophores to enter into the environment freely. There is little information regarding the dynamics of ionophores in the environment. This has been related to the lack of reliable, sensitive and robust methods that can measure their trace levels from complex environmental matrices like soil, natural water and animal manure. Studies show ionophore toxicity exhibited in flora and fauna, even reported in humans above the dose of 1 mg kg-1. Hence accumulation of ionophores in the environmental can be detrimental. Our multi-scale investigation of ionophores involved, a) method development for trace analysis of ionophores in poultry manure using liquid chromatography triple quadrupole mass spectrometry (HPLC-–MS/MS), b) batch equilibrium studies of ionophores using soils from mid-Atlantic region of the USA and c) influence of soil physico-chemical parameters on dynamics of ionophores in soil-water systems. Our HPLC-–MS/MS method was successful in quantifying ionophores ranging from (19.19 ±± 6.6) µg kg-1 to (97.86 ±± 19.19) µg kg-1 with concentrations of monensin being the highest. This method was further used to investigate partitioning of monensin in soil-ndash;water systems relevant to the occurrence of ionophores in the natural environment. Sorption and desorption isotherms were developed and influence of soil physico-chemical parameters on the sorption-desorption processes were analyzed. C-–type linear isotherms were generated with partition coefficients ranging from (6.41±± 1.34) to (343.83 ±± 5.68) LKg-1. Soil parameters such as cation exchange capacities, pH, organic matter, sand and silt content were found to correlate with sorption in different conditions. A major focus of this dissertation was to develop novel methodologies and design experiments to execute our research objectives.