Abstract：Endemic diseases in the lower Yellow River basin of Shandong Province, such as epidemic fluorine disease and endemic goiter, have impaired human health and economic development. Based on an investigation of the epidemic fluorine disease, endemic goiter and endemic arseniasis in four counties, in combination with the result of the eco-geochemical environment investigation, the authors studied the distribution and transformation of fluorine, iodine and arsenic in soils, potable water and crops. A comprehensive analysis of the relationship between eco-geochemical characteristics and endemic diseases was carried out. The results suggest that the epidemic fluorine disease has high positive correlation with fluorine content in soil and water. High content of iodine in water is the main cause of endemic goiter. The cause of endemic arseniasis remains unclear. According to the result of correlation analysis, this paper suggests canceling the supply of iodized salt in the high iodine area.