To address the conflicts of agricultural and ecological water use between the Shandong irrigation district and the Yellow River estuary, a method to evaluate the agricultural water-use security with the priority to meet ecological water demand is developed. A threshold analysis that takes into consideration evapotranspiration and effective rainfall is used to calculate irrigation water requirement. Then, a geo-statistical method is introduced to calculate irrigation water use for different regulatory regions with the priority to maintain different levels of environmental flows. Finally, a water-use security pressure index is introduced based on the geographic information system (GIS) platform, which is used to evaluate the spatial and temporal variations of water-use safety in the Shandong irrigation area. The results show that the maintenance of average and low levels of environmental flows could pose a pressure on agricultural water-use security for 33% and 27% of the average hydrological years, respectively. The corresponding pressure index is below 30% in most of the cases. The maintenance of a high level of environmental flows could pose a pressure on agricultural water-use security for 50% of the average hydrological years, with increases in the frequency and intensity of the pressure. In terms of spatial variations, the regulatory regions 2, 11, 13, 14 and 17 (i.e., Dayuzhang, Liuchunjia, Mawan and Bojili) are experiencing more stress than the other regulatory regions. When meeting the demand of low-level environmental flows, the pressure indexes are over 20% in these regulatory regions. With the average level of environmental flow demand, the pressure indexes are over 20% in most regulatory regions and over 30% in regulatory regions 2 and 13. When the environmental flow demand increases to the high level, the pressure indexes are over 60% in most regulatory regions. In water resources management and planning, the allocation target of environmental flows for the Yellow River estuary should be carefully adjusted according to the changing hydrological conditions and the spatially-varied meteorological factors. An improved distributed allocation plan could reduce the water shortage from 5.53 to 1.83 billion m³ while meeting the average demand of environmental flows in average hydrological years. The evaluation method developed in this study can reflect the spatial and temporal variations of agricultural water-use security when ecological water demand is satisfied in priority. It can effectively mitigate the conflicts between agricultural and ecological water demands and provide a decision-making basis for water resources management.