In this study, soil salinisation was investigated under a newly evolving irrigation practice, called partial root drying (PRD), which was used for irrigation of tomato and cotton. Under the PRD technique, a reduced amount of water compared to full plant water requirement was applied to one half of the plant root zone and leaving the other half dry. The wetting and drying halves of the root zone were alternated in subsequent irrigations. Greenhouse-grown tomato was drip irrigated, but field-crop cotton was furrow irrigated. Three irrigation treatments were tested for cotton grown in 2000: (1) FULL irrigation, the control treatment where the plant water requirement was fully met and water was applied to all sides of the plant root zone, as traditionally practised, (2) 1PRD and (3) 2PRD where irrigation water applied was reduced by 50% compared to FULL irrigation. The wetting and drying parts of the root zone were alternated every irrigation under I PRD, whereas it was alternated every other irrigation under 2PRD. For tomato, the 2PRD treatment was replaced with conventional deficit irrigation (DI) which again received 50% less water compared to FULL irrigation, but water was applied to all sides of the root zone, as practised under FULL irrigation. Soil water status of the plant root zone was continuously monitored with a neutron water gauge and tensiometers. Two sets of salinity measurements, at the start of the season and at harvest, were used to assess soil salinity. In addition to crop yield data, soil-salinity profiles and plant root zone isosalinity maps, constructed at harvest, were used to assess salt accumulation differences influenced by different irrigation treatments. The results showed that differences in salt accumulation were limited to only the surface layer of 30 and 20 cm depth for cotton and tomato, respectively, and the soil salinity at harvest under the PRD effect was 35% higher compared to FULL irrigation for tomato and cotton. The maximum salt accumulation encountered in the cotton field and greenhouse soil was 1.3 and 7.5 dS m(-1) respectively. Salt accumulation resulting under the PRD effect in the field was in no case higher than salt tolerance threshold levels of common field crops, including cereals, cotton and the like. Increase of salt content in the greenhouse soil was independent of the irrigation treatments used, and the accumulation mostly occurred within surface soil of 20 cm depth. The salt accumulation observed in tomato plots did not reach, in any case, tomato salt tolerance threshold level. However, the greenhouse soil needs leaching, as regularly practised, for the following year's crop. In this respect, the PRD practice and conventional DI do not require additional salt leaching over what is normally practised under FULL irrigation to sustain soil fertility. Therefore, one can conclude that the PRD practice should be valued equally with conventional DI for increasing crop water use efficiency with the least salinisation risk. Copyright (c) 2006 John Wiley & Sons, Ltd.