We investigated whether enhanced nitrogen (N) and water inputs would redistribute the microbial community within different soil aggregate size classes in a field manipulation experiment initiated in 2005. Distribution of microbial groups was monitored in large macroaggregates (> 2000 mu m), small macroaggregates (250-2000 mu m), and microaggregates (< 250 mu m) in a semiarid grassland. Both arbuscular mycorrhizal (AM) fungi and saprophytic fungi were the most abundant in soil macroaggregates. The gram-negative bacteria were more abundant in soil microaggregates. Total phospholipid fatty acid (PLFA) concentration in general and actinomycetes in particular decreased with N addition under ambient precipitation but was unaffected by combined additions of N and water within the three soil aggregate fractions as compared to control plots. In contrast, the abundance of saprophytic fungi decreased with combined N and water addition, but it was not affected by N addition under ambient precipitation. The abundance of gram-positive bacteria increased with N addition under both ambient and elevated water conditions for all soil aggregate fractions. In summary, the higher short-term nutrient and water availabilities provoked a shift in soil microbial community composition and increased total PLFA abundance irrespectively of the level of soil aggregation. In the long term, this could destabilize soil carbon pools and influence the nutrient limitation of soil biota within different soil aggregate size classes under future global change scenarios.