This research study investigates the way that soil organisms exist and interact with their physical environment. We are fundamentally interested in the soil physical and biological properties resulting from different long-term agricultural management decisions and the relationship between these physical and biological entities. The field site was located in the Appalachian Mountains of North Carolina at the Mountain Horticultural Crops Research Station on a fine-sandy loam soil. These treatments had been in place for nine years when this study was initiated; we believe this time period is sufficient to approach a steady-state natural system. The agricultural treatments investigated were a factorially-designed study with a whole-plot tillage treatment (conventional tillage vs. strip-tillage), a whole-plot input treatment (conventional chemical fertilizers and pesticides vs. organic fertilizers and pest control) and a split-plot rotational crop treatment (3-year vegetable rotation vs. continuous stake tomatoes). We examined soil aggregate stability, bulk density, and pore size distribution as representative physical properties. Soil respiration, nitrogen mineralization, enzyme activity, microbial biomass, and microbial, nematode, and earthworm community composition were used as representative biological soil properties. The measurements for respective properties were analyzed statistically using principle components analysis, redundancy analysis, and multivariate linear regression to determine correlations and consequent relationships between physical and biological components resulting from the implemented production treatments. We determined that the most important treatment factors affecting the soil biological community structure in agricultural ecosystems were, in order of importance, tillage, input, and rotation. We also determined that the most significant physical properties correlated to the biological activity of the soil agroecosystem were, in order of importance, microporosity and aggregate stability.