Irrigated agriculture has contributed to increasing topsoil acidity, which in turn can increase acidification of the subsoil. Lime is typically applied at a uniform rate to raise the pH of the soil, with no accounting for the variation in soil acidity that may exist within a field. Current commercial sampling protocols use surface soil composites taken across the whole field or in parts of fields where visual soil differences are apparent. Current liming recommendations may not account for in-field soil pH spatial variability, especially if the variability is not related to visual differences. Three studies were undertaken over 10 fields, to investigate the potential of using electro-magnetic induction instruments (Geonics EM38 and EM31) to target soil sampling in order to identify differences in soil acidity within flood-irrigated fields in southern New South Wales (NSW), Australia. Within individual fields, large differences in surface soil acidity were identified and a strong relationship (r² = 0.49 to 0.91) between the soil’s apparent electrical conductivity and soil pH was found. It is proposed that fields from southern NSW that have grown rice, be divided into zones to soil sample for acidity assessment, based on EM instrument readings. Proposed ECa levels for the delineation of zones are <80, 80–140 and >140 mS/m for EM31v and <80, 80–110 and >110 mS/m for EM38v. Many rice growers in southern NSW currently have EM maps of their fields. Using these maps to target soil sampling for soil acidity would be a more cost-effective method of determining the spatial variability of soil acidity in a field than grid sampling. Knowledge of the variability of soil acidity within the field would potentially allow the application of appropriate lime rates, relative to soil pH and cation exchange capacity to all parts of the field. This knowledge could make the variable application of lime a cost effective approach, compared with whole field management approaches.