AbstractIrrigation increases agricultural productivity and inevitably affects soil properties. When irrigation water is of a good quality and does not cause soil salinity or sodicity or contamination, and when there is no soil erosion, a gradual increase in soil fertility under irrigation conditions is, as a rule, expected. However, studies in various countries present examples of a gradual decline in soil fertility under long‐term freshwater irrigation due to leaching of organic matter and exchangeable cations. It is known that ploughing and agricultural activities modify natural soil formation processes and soil fertility. Irrigation enhances soil formation processes but also causes soil leaching. This paper presents data on the impact of long‐term freshwater irrigation on soil fertility for different climatic zones of Mexico, assessed by comparing some agrochemical properties of irrigated and non‐irrigated soils. This comparison shows that irrigation generally has a positive effect on soil fertility in arid conditions and a negative effect in semi‐arid, semi‐humid and humid tropical zones. Therefore, when planning and applying irrigation to crops, it is necessary to take into account not only crop water requirements, but also the need to preserve and improve soil fertility. © 2019 John Wiley & Sons, Ltd.