This study aims to evaluate the seasonal and spatial characteristics of hydrochemistry and DO isotopes and identify the eco-environmental threats under the background of saline intrusion and human activities in Yellow River Delta (YRD). Analyses for major ions (i.e., K+, Na+, Ca2+, Mg2+, SO42−, HCO3− and Cl−), nitrate ion (NO3−) and isotopic composition are performed for precipitation, river water, wetland water and sea water. Based on the range of δ2H and δ18O as well as their relations, the mixing between multiple sources and evaporation are confirmed. Electrical conductivity (EC), concentration of NO3−, soluble sodium percentage (SSP) and magnesium hazard (MH) are employed as indicators to reflect the ecological risks from salinity, agricultural pollutants, sodium and magnesium. By hierarchical cluster analysis (HCA), the samples of wetland water are grouped associated with those of river water. The characteristic reflects 3 patterns of risks in wetlands, including saline intrusion, human activities and their mixed influence.