This paper explores the effect of varying agricultural management practices on different water efficiency indicators: irrigation efficiency (IE), crop water use efficiency (WUE), and green and blue water footprint (WF). We take winter wheat in an experimental field in Northern China as a case study and consider a dry, average and wet year. We conducted 24 modeling experiments with the AquaCrop model, for all possible combinations of four irrigation techniques, two irrigation strategies and three mulching methods. Results show that deficit irrigation most effectively improved blue water use, by increasing IE (by 5%) and reducing blue WF (by 38%), however with an average 9% yield reduction. Organic or synthetic mulching practices improved WUE (by 4% and 10%, respectively) and reduced blue WF (by 8% and 17%, respectively), with the same yield level. Drip and subsurface drip irrigation improved IE and WUE, but drip irrigation had a relatively large blue WF. Improvements in one water efficiency indicator may cause a decline in another. In particular, WUE can be improved by more irrigation at the cost of the blue WF. Furthermore, increasing IE, for instance by installing drip irrigation, does not necessarily reduce the blue WF.