The Lluta valley in northern Chile is a hyper-arid region with annual precipitation lower than 1.1 mm, and high levels of boron (B) from alluvial deposits are present together with other salts that originated from the Cretaceous. Under these abiotic conditions, the ‘lluteño’ maize (Zea mays L.) is of interest because it has adapted to the Lluta valley with high salinity levels and B excess in the soil and irrigation water. Water and salt stress coincide in heavily irrigated hyper-arid agricultural areas, yet they are usually studied in isolation. We investigated in field conditions the combined effects of drought (22 days with no irrigation) under salinity (ECe: 5.5 mS cm−1; Na+: 17.8 meq L−1) and B (21.1 meq L−1) stress on physiology, growth, yield, and hourly water relations. The results allow to hypothesize that the measurement of the pre-dawn water potential represents the balance between the water potential of the soil and the root. Besides, under drought a significant effect of irrigation and time interaction was observed presenting a high differential between the leaf and stem water potential in both phenological stages. Furthermore, a decrease in net assimilation was observed, and it could be explained in part by non-stomatal factors such as the high radiation and temperature observed at the end of the season. Despite the drought, the cobs did not present a significantly lower quality compared to the cobs of plants without stress.