In this paper, based on the characteristic of natural geography, hydrometeor, ecological environment and the development of economic and society on the Qilu Lake Basin, making full use of a lot previous data, including field measured data, investigation data, planning reports and historical materials, to study and analyze the evolution population, arable land, irrigation area, agricultural planting, the water surface of lake of Qilu Lake since 1280 A.D. The test was carried out in the variation trend of Qilu Lake’s precipitation, average temperature, relative humidity, reference crop evapotranspiration, water resources, and other factors during 1950∼2016. The results show that water resources shortage phenomenon of Qilu Lake Basin can be traced back to 400 years ago. Social progress and increasing population have promoted the continuous improvement of the agricultural replanted pattern, the large consumption of water resources and the pollution of agricultural non-point sources have caused the deterioration of the water environment of the Qilu Lake. Additionally, lake water appears three times greatly atrophy was caused by the reclaiming land from lakes and climate warming, and the fragility of water ecology is intensifying. The integration of resources should be combined with the system of lake-leader, then taking some measures like that saving water and reducing wastewater, reducing agricultural replanting index, delineation of ecological red line and management and protection of water coastline, water trans-valley project form other river basin, allocation of water resources and monitoring and control of water resources and so on. The adoption of these measures will gradually repair the water ecology, improve the water environment, improve the carrying capacity of water resources, and realize the green and beautiful countryside.