We evaluated the spatial and temporal variation in the eco-environment of a mariculture area in Dapeng Cove, China using chemometric techniques and principal component analysis (PCA), clustering analysis (CA), and categorical principal component analysis (CATPCA). PC1 was associated with temperature, salinity, dissolved inorganic nitrogen (nitrate, nitrite, and ammonium), water sulfide, chlorophyll a and particulate organic matter, reflecting the influence of the seasonal transition of climate and hydrology. PC2 was characterized by phosphorus and sediment sulfide, primarily due to self-pollution from fish cage farming. PC3 was characterized by dissolved oxygen and chemical oxygen demand, related to the oxygen metabolism of cultured animals. PC4 was characterized by sediment organic matter, related to the biodeposition effect of oyster raft farming. The spatial-temporal variation in the eco-environment of the mariculture area were primarily affected by the subtropical monsoon climate combined with spatial and seasonal changes in the artificial production of caged fish and oysters.