Soil quality has been proposed as a prime indicator for characterizing and defining management factors contributing to soil degradation. In this study, biological (soil respiration, fluorescent Pseudomonas bacteria and entomopathogenic nematode populations), chemical (pH, inorganic N, and total C & N), and physical (bulk density and infiltration) indicators were used to determine soil quality. The specific research objective was to determine the capacity of this specific set of indicators to assess soil quality and determine its ability to detect short-term changes in soil conditions and processes. The assessment was comparative because of the lack of specific criteria or guidelines available in the literature for interpretation of most soil property indices measured. The following treatments were chosen from an ongoing farming systems study to achieve a preplanned set of comparisons that would make this type of assessment possible: (1) best management practices/conventional tillage (BMP/CT), (2) BMP/no-tillage (BMP/NT), (3) an organic system, and (4) a successional fallow system. Assessments were made multiple times between 1999 and 2000. Statistical differences between systems were found for all soil quality indicators except for entomopathogenic nematodes. Differences between systems varied across dates, a result that supports other research stating the need to consider the temporal variability of these indices for an unbiased overall soil quality assessment. Differences in total carbon and total nitrogen between systems were most evident in the 2000 sampling dates with BMP/NT showing greater contents on the last sampling date. The soil pH and inorganic N results did not suggest a possible difference in soil function status between any of the three agricultural systems studied. All three agricultural systems, BMP/NT, BMP/CT and organic, had similar pH values and overall low soil inorganic N levels. The non-agricultural successional system had a slightly more acidic soil condition than the three agricultural systems. Soil bulk density increased with time in the untilled BMP/NT and successional systems but the resulting values were not considered detrimental to either productivity or environmental quality. Infiltration was lower in the BMP/NT and successional systems than in the BMP/CT and organic systems. In conclusion, all soil quality indicators except for entomopathogenic nematodes proved to be sensitive to the detection of rapid changes in soil conditions that occur by the influence of soil management. The importance of using soil bulk density to express soil results on a volume basis, as the soil exists in the field before sampling, prevented an average interpretation error of 7–14% as compared to treatment comparisons on a soil weight basis only. This also demonstrates the need to carefully consider field sampling locations (row, between row, or wheel traffic areas) which dramatically influence soil density, physical characteristics, organic matter concentrations, and biological activity. Failure to consider these factors can invalidate even the most careful approaches to establishing baseline soil quality levels in the field as affected by various tillage and residue management practices and associated comparisons in time.