It is well known that multiple interactions can occur between nitrogen and water use, depending on climate, soil and crop characteristics, in crop growth and yield development. However, little is known about the simultaneous change in both water and N use efficiency (WUE and NUE) and their possible interactions in cereal–-legume intercropping systems. In order to advance our knowledge on the N and water facilitation mechanisms involved in the intercropping responses of N and water input co-limitations, we investigated, via four experiment years, the simultaneous optimization of water and N-fertilizer inputs, as well as its possible effects on growth, yield, N acquisition, and the NUE and WUE in intercropped species. The results indicated that intercropping increases the leaf area index by more than +0.14 and +1.03 units when compared to durum wheat and chickpea monoculture systems, respectively. This increase is particularly noticeable under higher rainfalls during the crop period (i.e., as can be seen in the 2022, 2020, and 2019 seasons). Moderate N-application enhanced both the grain yield and protein accumulation in the mixed crops by more than 0.22 t ha−1 and 57 kg ha−1, respectively. Conversely, intercropping significantly decreased the mixed grain yield when compared to durum wheat monocultures. Intercropping advantages in terms of biomass (ranged from 1 to 44%) and N-acquisition (2 to 91%) was confirmed in either low- (2021) or high- (2019 and 2022) rainfall growing periods, but only under low and moderate N-applications. Improving N nutrition under both rainfall and drought growth periods was confirmed only for the mixed crops under all applied N-fertilizer doses. Such improvements in growth, N acquisition, and yield quality were most likely achieved by positive interactions (r2 = 0.73, p ≤ 0.001) between the NUE and WUE for the chickpea–wheat intercropping. Thus, 0.62 kg m−3 of WUE promotes a significant increase of 1 kg kg−1 in NUE by mixing chickpea-durum wheat. Rain-fed chickpea-durum wheat intercropping provides a higher performance in growth and yield quality compared to sole cropping systems; this may occur from the simultaneous optimizations of both water and N fertilizer inputs in low-N soil under semiarid conditions.