Incidence of blossom-end rot (BER) of tomato is known to increase with increasing salinity in hydroponics and field tomato crops due to osmotic stress and imbalanced ionic ratio in the media solution. The present investigation evaluated salinity effects on the occurrence of BER of tomato in a completely closed root environment known as the closed insulated pallet system (CIPS). The CIPS is a continuous sub-irrigation capillary system with water moving from reservoir to rootzone in response to plant uptake and loss through transpiration and growth. In CIPS, fertilizer reserve is placed at the top surface of the root matrix, so fertilizer ions move downward by diffusion. Various tomato genotypes were seeded directly into CIPS in Spring. The experiment was terminated at a 100-day growing period. The incidence of BER was calculated as percent affected fruits. Salinity treatments consisted of five concentrations ranging from 0 to 10 g/L NaCl. One salinity treatment was 1 g/L CaCl2. In CIPS, the salt gradient created by uptake of saline water had lowest concentration at the top of root compartment where fertilizer was placed. Therefore, there was minimal ionic interactions between fertilizer ions and ions from the saline water. The uptake of water and plant growth decreased with increasing salinity concentration. The addition of Ca in the sub-irrigation water had no effect on the occurrence of BER. The incidence of BER correlated negatively with salinity level and plant growth in the CIPS.