In semi‐arid Mediterranean soils, water availability is the most limiting factor, negatively affecting the organic matter (OM) degradation. The aim of this work is to study under controlled laboratory conditions how three sources of OM [municipal solid waste (MSW), sheep manure (SM) and cow manure (CM)] behave when they are applied to an agricultural soil subjected to a severe year‐long drought. In order to apply the same concentration of OM to the soil (16·92 Mg OM ha−1), 2 kg of soil was mixed with 30, 67·41 and 55·25 Mg ha−1 (dry matter) of MSW, CM and SM, respectively. Two levels of irrigation were employed: (i) watered soils and (ii) non‐watered soils. Soil's chemical properties [water soluble carbon (WSC), humic acids, fulvic acids and protein mass distribution], biological properties (soil microbial biomass carbon and o‐diphenoloxidase activity) and solid‐state 13C cross‐polarisation magic angle spinning nuclear magnetic resonance spectroscopy were determined. In watered soils, the soil microbial biomass carbon was higher in the SM than in CM and MSW treatments (9·9% and 23·1%, respectively). The WSC was significantly higher in SM than in CM (55·7%) and MSW (78·7%) treatments. A decrease in the content of O‐alkyl C and an increase in alkyl C, aromatic C and carboxyl C were observed. In non‐watered soils, the biochemical properties and alkyl C and alkyl/O‐alkyl ratio decreased, whereas WSC content and O‐alkyl C increased. These results indicated that the evolution of OM and the activity of the microbial community in non‐watered soils were very different to those in the watered soils. Copyright © 2016 John Wiley & Sons, Ltd.