Rapid economic development has posed pressure on water resources, and the potential for a water crisis has become an important obstacle to the sustainable development of society. Water footprint theory and its applications in agriculture provide an important strategic basis for the rational utilization and sustainable development of water resources. Based on the monthly meteorological observations and agricultural data of Shandong Province, CROPWAT 8.0 and Geographic Information System (GIS) technology, the green, blue and grey water footprints of wheat, maize, cotton and groundnut from 1989 to 2016 were calculated and the spatial variations of water footprints for crops in different rainfall years were analyzed. Additionally, assessment of water stress for agricultural productions was conducted in this study. The results showed that the average water footprints of wheat, maize, cotton and groundnut were 2.02 m3/kg, 1.24 m3/kg, 7.29 m3/kg and 1.75 m3/kg, respectively in Shandong Province. A large amount of the average total water footprint was calculated for wheat (420.59 × 108 m3/yr), maize (222.16 × 108 m3/yr), cotton (72.70 × 108 m3/yr) and groundnut (50.07 × 108 m3/yr). The average total water footprint of the four crops was 765.52 × 108 m3/yr (29.98% blue) and exhibited a gradual decreasing trend over time. Specifically, the total water footprint of wheat was the highest among four main crops in Shandong Province and exhibited a decreasing trend during 1989–2016. The maize was ranked in the second place, and was the only crop still increasing rapidly. The spatial and temporal changes of water footprints for crops were obvious in different rainfall years. Additionally, agricultural productions in most regions were facing the threat of water scarcity. Therefore, the scientific planning of crop planting structures and rational control of sown areas of crops with large water footprints should be implemented in severely water-scarce regions. This study can give some suggestions on the adjustment of planting structure for the sustainable development of agriculture and the realization of efficient utilization of water resources.