We studied the responses of quinoa (Chenopodium quinoa Willd.) to single and combined effects of four different irrigation water salinity (electrical conductivity) levels (S1: 0.25, S2: 5, S3:10 and S4: 20 dS m− 1), and four water application rates (W1:120%, W2:100%, W3:70% and W4:50% of depleted water from field capacity), in a fully randomized factorial design with total of 48 weighted lysimeters. Seed yield was 30% higher when water requirement was fully met (W1 and W2) as compared to treatments where water requirement was partially met (W3 and W4). Crop water response coefficients were found sensitive (Ky= 1.55) to drought induced water stress but tolerant to salinity induced water stress (Ky=0.47). We found that quinoa had a salinity threshold value of ~ 4 dS m− 1 (in soil extract) with a slope of 3.4%, (yield loss per dS m− 1 increase in salinity) which is classified as moderately salt tolerant crop. We evaluated the combined effects of salinity and water levels on seed yield, concluding that if there is more than one stress factor, the crop will respond to the stress factor having the highest impact (either salinity or water stress). Seed yield under combined salt and water stress for all treatments was well predicted from the separate responses to water and salt stress using the dominant stress response model. Our results indicate that over the range of conditions studied, quinoa water productivity was more dependent on applied water rate than on salinity.