Agricultural practices that alter the soil organic matter (SOM) content are expected to cause changes in soil stability and aggregation. The objective of this study was to evaluate short‐term (<2 yr) changes in water‐stable aggregates (WSA) in a silt‐loam soil under different management regimes. The interactive effects of tillage (no‐till and conventional tillage), crop rotations (continuous corn, corn‐soybean rotation) and composted cattle manure applications [0, 15, 30, and 45 Mg (wet weight) ha −1 ] on WSA were assessed in a factorial (tillage × crop rotation) split plot (compost) experiment. The proportion of WSA >4 mm was greater in compost‐amended than unamended soils within 1 yr, and the mean weight diameter (MWD) of aggregates increased with increasing compost application rates. By the second year of the study, no‐till soils under continuous corn and the soybean phase of the corn‐soybean rotation had more WSA >4 mm and a greater MWD than any crop rotation in conventionally tilled soils. Increasing the C input to soil increased the MWD of aggregates. The MWD of aggregates was related to the C content of soils under no‐till, but not conventional tillage, suggesting more physical stabilization of organic matter (OM) in no‐till than conventional tillage agroecosystems. Our findings indicate rapid improvements in aggregation of a silt‐loam in the first 2 yr after compost application and the adoption of no‐tillage practices.