Carbonates constitute a significant proportion of the soil mass in many semi-arid soils. Due to their solubility, they can be affected by changes in the soil water regime. This needs to be taken into account when assessing the environmental and agronomical impacts of the adoption of irrigation. To gain knowledge on the importance of the effect of irrigation on carbonates dynamics in the tilled layer (0–20cm) of agricultural soils, we conducted a two-step study embracing field observations and numerical simulation. First, carbonates storage and their size distribution were quantified for two different situations (irrigation and non-irrigation) in three irrigation districts with different time under irrigation (Valtierra (19years), Miranda (5years) and Funes (12years)) in Navarre (Spain). Soil sampling was designed to ensure homogeneous comparisons in the most characteristic soil types at each site (Xeric Haplocalcid, Typic Calcixerept and Xeric Haplocalcid, respectively). Carbonates concentration was systematically lower with irrigation in the finest (<50μm) soil fraction: 22.2±1.4g carbonates 100g−1 fraction without irrigation for 16.1±0.9 with irrigation in Valtierra, 26.7±1.1 for 19.1±3.8 in Miranda and 27.8±2.9 for 22.7±1.5 at Funes1. However, the net annual balance of total carbonates-C between irrigated and non-irrigated condition was neutral at the three sites. This can be explained by agricultural management affecting carbonates in the sand-size fraction, including the addition of carbonates with fertilizers, and coarse carbonate particles brought to the surface by tillage.In a second step, a simplified model was developed for use with easily available data in most irrigation districts, and numerical simulations of the geochemical interactions between the soil, the soil solution and irrigation water were run using actual soil and soil solution data from the tilled layer of another pair of plots in Funes (Funes2). Sensitive analysis was also conducted to investigate the potential impact of water quality and crop types as sources of variability on the model outputs. The modelling results showed annual values of carbonates-C loss in the range between 13.52 and 12.06gm−2year−1 in the studied depth under irrigation, depending on the quality of irrigation water, for 0.46gm−2 without irrigation. These data were within the range of carbonates budgets found in the literature but one order of magnitude lower than the observed results in the fine fraction in the field. Overall, our results showed that irrigation can significantly alter carbonates dynamics in semi-arid Mediterranean land, which implies that human use can significantly alter the mineral phase of these soils in a relatively short time lapse. Simple geochemical models can be a useful approach to evaluate changes in the carbonates balance at the local and regional scale when irrigation is applied, although they have to be improved to account for other factors related to agricultural management and local geochemical conditions.