Enhancing soil organic carbon (SOC), nitrogen (N) and water use efficiency (WUE) are significant challenges in intensive wheat production. An intercropping system combining wheat and grain legumes may help maintain SOC, soil mineral N and WUE while also providing an opportunity to sequester carbon (C) in low input organic systems. We grew wheat (Triticum aestivum cv. ‘Scarlet’) as a monoculture and intercropped with either common bean (Phaseolus vulgaris cv. ‘Red Kidney’, or cv. ‘Black Turtle’), or fava bean (Vicia faba cv. ‘Bell’) in rows of 1:1, 2 wheat: 1 bean or broadcast arrangement without fertilizers for 2 years to assess the effects of genotype and spatial arrangement on biological nitrogen fixation and seasonal transfer, WUE, gross ecosystem photosynthesis (GEP), and net ecosystem productivity (NEP). Stable isotope methods (13C and 15N natural abundance) were used to quantify C and N within the plant and soil system. Field CO2 exchange measurements used a dynamic closed transparent chamber connected to a portable CO2 analyzer. Intercropped plots had higher percent N derived from symbiotic N2 fixation, and increased C and N accumulation compared to monocultured wheat. The fava bean cv. Bell intercrops showed increased nodulation (60–80 % more nodules) and percent N derived from symbiotic N2 fixation (10–12 % higher) compared to common beans resulting in the fixation of 74 kg N ha−1 biologically from the 1:1 arrangement. The highest rate of N-transfer (13 %) was observed in the wheat-fava bean cv. Bell combination when planted in the 1:1 arrangement. All intercrops accumulated more N in shoot biomass compared to monoculture wheat with wheat-fava bean cv. Bell (1:1 arrangement) accumulating the highest N (34 kg N ha−1, i.e., 176 % higher) and C (214 g C m−2 year−1, i.e., 26 % higher). All plots fixed the most CO2 (i.e., greatest GEP) during mid-growth stage (50 days after seeding i.e., prior to flowering) however, wheat-fava bean cv. Bell in the 1:1 arrangement displayed the greatest NEP sequestering C at the seasonal daytime average rate of 208 mg C m−2 h−1 (i.e., 7 % higher than wheat monoculture plots). Intrinsic WUE of wheat, as indicated by δ13C, was also improved when grown with fava bean cv. Bell or common bean cv. Red Kidney. This study demonstrated that intercropping wheat and fava bean is an effective strategy to achieve greater nitrogen fixation and transfer to the wheat counterparts, higher WUE, and ecosystem productivity than wheat monocultures in areas with low soil N and C. Furthermore, the wheat-fava bean cv. Bell (1:1 arrangement) was more productive than either the 2:1 or mixed planting arrangements.