Irrigation is known to influence soil organic matter dynamics and aggregation, but its effects are not completely understood. In this work, organic C inputs from crops and the topsoil (0–10 cm) organic fraction and aggregates size-distribution were measured during the two first growing seasons in an experimental field with four treatments: rainfed and irrigated wheat (Triticum aestivum L.), and rainfed and irrigated maize (Zea mays L.). Crops inputs were calculated from grain yields and harvest index data. The organic C stock was measured for an equivalent soil mass from C concentrations and bulk density. Aggregates size-fractions were obtained with a method based in the hierarchical model of aggregation. Maize-derived C incorporated was quantified using δ13C concentrations in soil samples, because maize residues have higher δ13C values than C3 plants. Despite some differences in yield, no differences were observed in total C inputs to the soil from crops and in organic C stocks or aggregate-size distribution. However, the proportion of maize-derived organic C was higher in irrigated than in rainfed plots (13.4% and 4.94%, respectively), and maize-C was observed to incorporate preferentially into large macroaggregates (2000–5000μm). Incorporation of maize-C in small macroaggregates and microaggregates (250–2000 μm and 50–250 μm) was observed only under irrigation, supporting the hypothesis that irrigation can change the incorporation and mineralization dynamics of crop residues into the soil organic pool and modify their distribution within the soil structure.