Agriculture is a key sector and a major consumer of water resources; therefore, a clear understanding of the agricultural water demand for crop production and consumption is imperative for addressing water scarcity problems, particularly in water export regions. This study provides new insights into the influential factors driving the changes in the agricultural production water footprint (WFprod) and consumption water footprint (WFcon) in the net water import and net water export regions. The WFprod and WFcon of wheat are evaluated in Beijing city (the net water import region) and Heilongjiang province (the net water export region) over the period 1996–2015. The statistical significances of the influential factors, i.e., climate change, gross domestic product, population, dietary demand and technology update are determined using a multivariate linear regression model (LRM) and nonlinear regression model (NLRM). The results indicate that the gross domestic product and population were the dominant positive influential factors, whereas technology update and dietary demand were the dominant negative influential factors affecting the changes in the WFprod and WFcon in the net water import region. In the net water export region, technology update was the dominant negative influential factor affecting the changes in the WFprod and WFcon. Climate change did not contribute significantly to the changes in the WFprod and WFcon of wheat; however, it was an important factor (especially precipitation for the green WF with an average relative importance of more than 22% and the blue WF with an average relative importance of more than 15%) affecting the changes in the WFprod and WFcon of the crop. An in-depth analysis of the influential factors that contribute to the changes in the WFs is fundamentally important for decision-makers to develop countermeasures and strategic planning implementations to mitigate water resource pressure in China.