The water footprint (WF) of crop production is a friendly approach for the analysis of water resource consumption in agricultural production systems. This study assessed the inter-annual variability of the total WF of three types of main crops, namely, cereal (i.e., spring wheat and barley), oilseed (i.e., canola and sunflower) and pulse (i.e., lentils and chickpea), from the perspective of yield and protein. It also determined the major factors that influence the WFs in Saskatchewan province of Canada. Over the period of 1965–2014, the annual precipitation in Saskatchewan fluctuated considerably but increased slightly with time. The grain yield-based WF ranged between 1.08 and 1.80, 0.90 and 1.38, 1.71 and 2.58, 1.94 and 4.28, 1.47 and 2.37, and 1.39 and 1.79 m3 kg−1; whereas the protein yield-based WF ranged between 7.69 and 10.44, 8.27 and 16.47, 3.79 and 7.75, 4.86 and 11.17, 5.09 and 7.42, and 5.51 and 10.69 m3 kg−1 for spring wheat, barley, canola, sunflower, lentils, and chickpea, respectively. All the WFs of crops generally decreased with time, which could be attributed to precipitation factors. In addition, the scientific and technological progress and agricultural inputs also evidently influenced the grain yield-based WFs of all crops. Pulse crops had a higher grain yield-based WF (an average of 1.59 m3 kg−1 for pulse crops and 1.18 m3 kg−1 for cereal crops) but a lower protein yield-based WF (an average of 6.58 m3 kg−1 for pulse crops and 9.25 m3 kg−1 for cereal crops) than cereal crops. Under conditions of improved protein consumption and healthy living in the future, pulse crops may be a preferred crop.