BackgroundPoly‐γ‐glutamic acid (γ‐PGA) can promote crop growth and improve soil properties efficiently. However, the optimal application rate of γ‐PGA in legume/non‐legume intercropping systems is still unclear. A potted experiment was conducted to investigate the effects of five γ‐PGA rates (0%, 0.1%, 0.2%, 0.3%, and 0.4%, represented by CK, P1, P2, P3, and P4, respectively) on biological nitrogen (N) fixation (BNF), water‐N productivity, and nitrate distribution in a cotton/soybean intercropping system.ResultsThe results showed that the growth indicators (plant height, stem diameter, leaf area index, root dry weight, root length) of cotton and soybean increased first and then decreased with increasing γ‐PGA rates, and all growth indicators of cotton and soybean showed peaks in P3 and P2 treatments. The stable 15N isotope method indicated that γ‐PGA promoted the BNF capacity of soybean and soil. In particular, the percentage of N derived from the atmosphere (Ndfa) in soybean reached 61.94% in the P2 treatment. Poly‐γ‐glutamic acid improved the water‐N productivity, and the total N partial factor productivity (NPFP) and water productivity (WP) in P3 treatment increased by 23.80% and 43.86% compared with the CK treatment. The γ‐PGA mitigation of potential nitrate residue also decreased first and then increased with increasing γ‐PGA rates.ConclusionMultivariate regression analysis showed that 0.22% of the optimal γ‐PGA application rate could obtain a higher yield and water‐N productivity in cotton/soybean intercropping system simultaneously. © 2023 Society of Chemical Industry.