The Yellow River Basin (YRB), the second largest river basin of China, has experienced a booming agriculture over the past decades. But data on variability of and trends in water consumption, pollution and scarcity in the YRB are lacking. We estimate, for the first time, the inter- and intra-annual water footprint (WF) of crop production in the YRB for the period 1961–2009 and the variation of monthly scarcity of blue water (ground and surface water) for 1978–2009, by comparing the blue WF of agriculture, industry and households in the basin to the maximum sustainable level. Results show that the average overall green (from rainfall) and blue (from irrigation) WFs of crops in the period 2001–2009 were 14% and 37% larger, respectively, than in the period 1961–1970. The annual nitrogen- and phosphorus-related grey WFs (water required to assimilate pollutants) of crop production grew by factors of 24 and 36, respectively. The green–blue WF per ton of crop reduced significantly due to improved crop yields, while the grey WF increased because of the growing application of fertilizers. The ratio of blue to green WF increased during the study period resulting from the expansion of irrigated agriculture. In the period 1978–2009, the annual total blue WFs related to agriculture, industry and households varied between 19% and 52% of the basin's natural runoff. The blue WF in the YRB generally peaks around May–July, two months earlier than natural peak runoff. On average, the YRB faced moderate to severe blue water scarcity during seven months (January–July) per year. Even in the wettest month in a wet year, about half of the area of the YRB still suffered severe blue water scarcity, especially in the basin's northern part.