There is a growing consensus on a need for comparing the cropland with a reference state or native land in a prime soil health state to determine soil health management goals in croplands. However, the complex soil heterogeneity and climate variations make soil health potential variable and confound the land-use and management practices while comparing soils from different sites. Identifying a discrete landmass unit where all soils have similar health potential will be instrumental in conducting meaningful comparative studies. This methodological paper proposes and discusses a land unit, Reference Ecological Unit (REU), that accounts for soil and climate variabilities and covers the area with similar soil health potential. The REU is developed for one Major Land Resource Area in Nebraska based on the USDA-NRCS hierarchical land classification system. A true difference in soil health for different land use and agronomic management practices such as no-till and cover crops can be determined by comparing sites within an individual REU. Evaluation of management effects on soil health indicators in an REU will adequately illustrate the beneficial impact of such practices without being confounded by agroecological variations.