Rapid decline in groundwater table due to excessive withdrawal of water for irrigation has been posing a serious threat to sustainable agricultural production in hot arid region of India. Alternative cropping systems having low irrigation requirement have been proposed to resolve unsustainable groundwater use but trade-off with other dimensions such as yield, profitability, and environmental impacts is not well-documented. An integrated analysis of amount of groundwater use, productivity, profitability, resource-use efficiency (RUE), and environmental impacts of three cluster bean-based cropping systems [conventional cluster bean (Cyamopsis tetragonoloba)–wheat (Triticum aestivum) (CB–W), and two alternative cropping systems, namely cluster bean-Indian mustard (Brassica juncea) (CB–IM) and cluster bean–blond psyllium (Plantago ovata) (CB–BP)] under different soil management practices [two tillage types, i.e., conventional (CT), and deep tillage (DT); and three farmyard manure (FYM) application rates, i.e., 0, 5, 10 Mg ha-1] was carried out. Based on a three-year field experiment, compared to conventional CB–W, alternative cropping systems produced 28.6–47.4 % lower seed yield, but enhanced economic returns (7.6–31.1 %), while reduced amount of irrigation (− 27.9 to − 37.2 %), energy (− 22.4 to − 37.0 %), and nutrient (− 17.4 to − 46.1 %) used, global warming potential (− 20.2 to − 45.9 %) and greenhouse gas intensity (− 27.3 to − 57.7 %). Alternative cropping systems saved 1.87–2.50 × 103 m3 per year per hectare of groundwater than conventional cropping systems. Soil management practices influenced agro-economic and environmental dimensions of cropping systems. Deep tillage (DT) enhanced yield (14.0 %), economic profit (18.8 %), RUE (13.2 %, 13.8 % and 8.5 % for nutrient, water and energy use efficiency, respectively). Addition of FYM increased yield (up to 23.0 %), economic net return (up to 21.8 %), RUE (up to 22.7 %, 16.5 %, 91.0 % in water, energy and nutrient use efficiency), and reduced global warming potential (up to − 7.9 %). The CB-BP cropping system with DT and FYM addition offered the best balance of yield, profit, saving of irrigation water, energy and nutrient, while minimizing GWP. This study provides empirical evidence of the opportunities for alternative cropping systems which balance the multiple objectives of sustainable groundwater use, farmer profitability and environmental sustainability for arid region of India. The results have direct implications for sustainable utilization of underground water for similar regions of the world facing water shortage.