Agricultural water consumption is the main contributor to water scarcity worldwide, while small-scale and large-scale agriculture have distinguishing characteristics. Significant gaps remain in the process-based agricultural production and water consumption estimates distinguishing small-scale and large-scale agriculture, which inhibits our deep understanding of where, how, and by whom crops are produced and against what water outcomes. We close this gap by leveraging a gridded crop model, covering 61% of the global harvested area using a 2010 baseline. Results show small-scale agriculture accounts for 43% of the total harvested area, however, contributes to relatively less nutrient production despite cultivating more food crops (relative to their total harvested area) than large-scale agriculture. This result challenges the assumption made by existing global scale studies when allocating national agricultural production to small-scale and large-scale agriculture, which (partly) ignores the differences in climate conditions, soil characteristics, input level, and type of irrigation that small-scale versus large-scale agriculture may have. The lower contribution is due to both water and soil fertility stress. Small-scale agriculture overrepresents in water-scarce regions but consumes much less blue water (38%) compared to its harvested area (54%). In water-scarce regions, soil fertility stress causes small-scale agriculture the unproductive green water utilization and a 70–90% unmet crop production potential. Our findings demonstrate the unequal exposure and contribution to water scarcity between small-scale and large-scale agriculture and between food and non-food crops. Understanding such disparities is one of the first and necessary steps toward enhancing the resilience and sustainability of agricultural systems.