This comprehensive two-year field study investigates the transformative potential of sub-surface drip fertigation (SSDF) as a sustainable alternative to traditional surface flood irrigation coupled with manual nutrient broadcasting in the cotton-wheat cropping system (CWCS). The field experiment was laid out in a split-plot design with combination of two lateral depths (25±2.5 and 30±2.5 cm) and two emitter spacings (30 and 40 cm) in main plots and four fertigation schedules [100% Recommended nitrogen (RDN)-112.5 kg N ha−1) and 125%RDN in 10 &14 equal splits (cotton); 100% Recommended nitrogen and phosphorus (RDNP)-125:62.5 kg NP ha−1) and 80%RDNP in 08 & 10 equal splits (wheat)] in sub plots.Two additional control treatments i.e., C1[Surface flood (SF) irrigation with 100%RDN (105 kg N ha−1 for cotton), 100%RDNP (125:62.5 kg NP ha−1for wheat) applied through manual broadcasting] and C2[SSDF at 20±2.5 cm depth, 20 cm emitter spacing, and 100%RDN for cotton(112.5 kg N ha−1) in 10 equal splits, and 80%RDNP for wheat (100:50 kg NP ha−1) applied in 8 equal splits] were also studied.Results revealed an 18.6% improvement in CWCS productivity under SSDF, when cotton and wheat were fertigated with 125%RDN in 14 equal splits and 100%RDNP in 10 equal splits, respectively in comparison to 100%RDN in 10 equal splits (cotton) and 80%RDNP in 08 equal splits (wheat). Furthermore, lateral placement (25±2.5 cm) depth with emitter spacing (30 cm), and fertigation [125%RDN in 14 equal splits (cotton) and 100%RDNP in 10 equal splits (wheat)] improved crop, irrigationand total water productivity indices by 1.3, 3.1, and 2.1 folds, respectively as compared to SF (C1). Moreover, improvednet returns by 18.7–52.0%was also evident with a SSDF of 100%RDN in 14 equal splits and 80%RDNP in 10 equal splits in cotton and wheat.These findings elucidated that SSDF with drip lateral placement at 25±2.5 cm depth, having an emitter spacing of 30 cm, and fertigation of 125%RDN (140 kg N ha−1) in 14 equal splits(cotton); 100%RDNP (125:62.5 kg NP ha−1) in 10 equal splits (wheat) could be a novel water-savvy concept in sustaining the yield and water productivity of cotton-wheat cropping system under arid agro-ecosystems.