Abstract: This dataset is built from physical and chemical data archives of the Jiaozhou Bay Marine Ecosystem Research Station during 2006-2010. Covering seven parameters (water temperature, salinity, ammonia nitrogen, nitrate, phosphate, silicate, nitrite), it contains analysis data from 1216 samples collected quarterly in standard depth layers at 10 routine monitoring sites in the Jiaozhou Bay. Data quality control was carried out during sampling and analyzing processes following general national and international standards. The system integrity of this dataset favors interpretation of environmental variabilities on temporal and spatial scales, and provides scientific and data support for ecosystem health evaluation and environment protection in the Jiaozhou Bay.