Soil samples were collected to a depth of 10 cm in 1991 and 1993 in a vegetable crop rotation experiment initiated in 1989. The two cropping treatments (under either 0 or 280 kg N ha(-1)), were the traditional vegetable rotation (TVR) currently being practiced and an alternative rotation (LVR) in which a vegetable crop alternated with a legume, red clover (Trifolium pratense L.), that was incorporated as green manure the following spring. Chemical and microbiological parameters were determined on whole soil and five soil aggregate size fractions: 1.00-2.00, 0.50-1.00, 0.25-0.50, 0.10-0.25, and less than 0.1 mm. Within a 2 year period, there was a major shift in the natural fabric aggregate size distribution in the LVR with a 35% decrease in microaggregates ( < 0.25 mm) and a similar percentage increase in macroaggregates ( > 0.25 mm). On the whole soil, the shift was accompanied by large increases in the microbial biomass to soil C ratio (C-mic:C-org) and microbial biomass (C-mic). Furthermore, labile organic matter pools (particulate organic matter and dissolved organic C) were significantly (P < 0.05) higher in the LVR than TVR soils in both sampling years. Large aggregates had a high C-mic, C-mic:C-org and low qCO(2) (mg CO2-C mg(-1) C-mic). There was a negative correlation (r = 0.713***) between qCO(2) and aggregate size, and a positive correlation of C-mic or C-mic:C-org with aggregate size (r = 0.76*** and r = 0.74** respectively). Nitrogen fertilization caused a general increase in qCO(2), CO2-C and C-mic. The results documented a significant improvement of soil aggregation and maintenance of organic C pools with a soil management system that provides greater root activity and C input. Further, the results indicated that there was a qualitative difference in microbial communities between macroaggregates and microaggregates.