With a renewed interest and demand in organic products, organic agriculture has become one of the fastest growing industries in the US. Organic farmers rely on non-chemical methods to build soil fertility including crop rotations, green manures, and animal manures. One concern with continued and excessive use of animal manures over the years is potential buildup of soil salinity and its adverse impact on farm productivity and sustainability. Irrigation can leach the salts down from the soil surface and may lead to accumulation of salts in deeper soil depths. Objective of this study was to investigate salinity and related properties of furrow or flood irrigated soil at various depths under several years of organic farming in southern New Mexico. Soils were collected and analyzed from 0-30, 30-60, 60-90 and 90-120 cm depths from three organic fields that were under certified organic for 11 years (OF11), 14 years (OF14) and 17 years (OF17), along with a neighboring conventional field as a control (CON). Soil salinity, expressed as the EC in the saturated paste extract, changed significantly with increasing soil depths for all the farms. Broadly, the conventional farm had lower soil EC than the organic farms. Soil sodicity levels, assessed as the sodium adsorption ratio (SAR) of the saturation extract of the soil, within the 0-120 cm soil profile at all the organic farms were generally higher than the conventional farm, with the differences being significantly higher under the oldest organic farm OF17 at different soil depths as compared to the conventional farm. There is a need to regularly monitor soil salinity and sodicity levels and implement a management plan to prevent excessive build-up of salts under the organic farming systems.