In higher plants, due to indiscriminate use of fertilizers, sometimes multiple deficiencies or toxicity is created in the growing medium, which disturbed the yield and metabolism of plants. To observe the effect of sulphur (S) deficiency on zinc (Zn) and boron (B) nutrition of mustard (Brassica compestris L.) var. T9, plants were grown in refined sand in complete nutrition (control - 2 mM S, 1 µM Zn and 3 µM B), low S (0.02 mM), low Zn (0.01 µM), low B (0.3 µM), low S-low Zn, low S-low B, low Zn-low B, and low S-low Zn-low B. The deficiency of S decreased the biomass, seed yield, concentration of chlorophyll, S and B, Hill reaction activity and increased the concentration of Zn, accumulation of carbohydrates and activity of starch phosphorylase, peroxidase, acid phosphatase and carbonic anhydrase. The magnitude of Zn deficiency effects were accentuated by low S and were reversed to large extent by low B. The parameter that were affected are, intensity of visible symptoms of low Zn, biomass, seed yield, concentration of chlorophyll and Zn, activity of peroxidase, acid phosphatase, carbonic anhyrdrase and accumulation of sugars and starch. Similarly the effect of low B, increase in symptoms of B deficiency, reduction in biomass, seed yield, concentration of B, chlorophyll and increase in the activity of peroxidase, acid phosphatase and starch phosphorylase were aggravated by low S and mitigated to the same extent by low Zinc. These results revealed a synergism between S and B as well S and Zn and antagonism between Zn and B.