This dataset is built on the hydrological and chemical data archives of the Jiaozhou Bay Marine Ecosystem Research Station during 2006-2010 at 10 routine monitoring sites in the Jiaozhou Bay. Covering seven parameters (water temperature, salinity, ammonia nitrogen, nitrate, phosphate, silicate and nitrite), it contains the analysis data from 1,216 samples collected quarterly (in February, May, October and November) in accordance with the standard water depth layers. We carried out data quality control for the monitoring environmental factors during sampling and analyzing processes by following general national and international standards. The system integrity of this dataset can favor interpreting the physical and chemical environmental variabilities of water on temporal and spatial scales, and provide scientific basis and data support for ecosystem health evaluation and environment protection in the Jiaozhou Bay.