The increase of water temperature, due to thermal discharges from two nuclear power stations, was one of the most significant environmental changes since 1982 in the Daya Bay, located in the north of the South China Sea. This study investigates the long-term (1982-2012) environmental changes in Daya Bay in response to the increase of water temperature, via comprehensively interpreting and analyzing both satellite and in situ observations along with previous data. The results show that: 1) salinity, dissolved oxygen (DO), chemical oxygen demand (COD) and nutrients had been enhanced after the thermal discharges started in 1994; 2) the concentration of Chl-a increased while the net-phytoplankton abundance decreased; 3) diversity of the phytoplankton community had decreased; 4) fishery production had declined; and 5) frequency of Harmful Algal Bloom occurrence had increased. Satellite images show clearly that a thermal plume from the power stations extended toward the interior of Daya Bay, and that surface temperature of the seawater increased as one approached the power stations. The analysis suggests that the thermal water discharged from the two power stations was a driver of the ecosystem's change in Daya Bay. Several factors, including nutrients, salinity, DO, and COD, varied according to the increase of water temperature. These factors affected the water quality, Chl-a, and phytoplankton in the short term and impaired aquatic organisms and the whole ecosystem in the long term.