The Yellow River Delta (YRD) is a typical case of frequent interaction between surface water and groundwater under the seasonal flow-sediment regulation regime. A total of 40 samples (20 surface water samples, 19 groundwater samples, and 1 seawater sample), were collected during the high flow (October, 2019). Trace metals, hydrochemical indicators (EC, pH, major ion of Na+, K+, Mg2+, Ca2+, Cl−, SO4 2−, and HCO3 −) and stable isotopes (δ18O and δD) were determined. The impact of water diversion on the hydrochemistry of groundwater was significant, accounting up to a 90% of river discharge in some sites calculated by 2-component mixing model. Factor analysis indicated that Fe, Mn, Al, and B in surface water were closely correlated and were present in the dissolution phase due to sediment remobilization controlled by flow-sediment regulation; Sr was influenced by the dissolution of evaporate salt, while Ba suffered precipitation in the oxidation processes. However, the source of Sr, Mn, B, and Fe in groundwater was accompanied by hydrochemical compositions and per cent surface water, implying that the trace metals in surface water contributed to that of accumulation in the shallow aquifer; Al was influenced by plagioclase weathering, while Ba precipitated too.