India is one of the world's largest food producers, making the sustainability of its agricultural system of global significance. Groundwater irrigation underpins India's agriculture, currently boosting crop production by enough to feed 170 million people. Groundwater overexploitation has led to drastic declines in groundwater levels, threatening to push this vital resource out of reach for millions of small-scale farmers who are the backbone of India's food security. Historically, losing access to groundwater has decreased agricultural production and increased poverty. We take a multidisciplinary approach to assess climate change challenges facing India's agricultural system, and to assess the effectiveness of large-scale water infrastructure projects designed to meet these challenges. We find that even in areas that experience climate change induced precipitation increases, expansion of irrigated agriculture will require increasing amounts of unsustainable groundwater. The large proposed national river linking project has limited capacity to alleviate groundwater stress. Thus, without intervention, poverty and food insecurity in rural India is likely to worsen.