Open-lot cattle feeding operations face challenges in control of nutrient runoff, leaching, and gaseous emissions. This report investigates the use of precision management of saline soils as found on 1) feedlot surfaces and 2) a vegetative treatment area (VTA) utilized to control feedlot runoff. An electromagnetic induction soil conductivity meter was used to collect apparent soil electrical conductivity (ECa) from feedlot pens and a research VTA at the U.S. Meat Animal Research Center, Clay Center, Nebraska. An ECe Sampling Assessment and Prediction (ESAP) program, developed by the Soil Salinity Lab at Riverside, California was used to analyze feedlot pens and the VTA. The program directed soil sample site locations and produced models associating ECa to volatile solids (VS) and chloride (Cl−, an indicator ion for feedlot runoff). Results from the feedlot site for two pens with differing management styles indicate positive correlations between ECa and associated VS (R2 = 0.90, soil mound pen; R2 = 0.65, manure mound pen). Chloride was found to be associated with ECa for the VTA (R2 = 0.81). The ESAP program provided estimates of the secondary variable distribution across the VTA and feedlot pens based on soil sample data combined with high density soil conductivity (ECa) data. The methodology outlined in this research will be useful for identifying areas of excessive nutrient buildup on feedlots and runoff control areas, thereby allowing for site-specific management, improvement of system performance, and sustainability while reducing nutrient losses to the environment.