The chain-forming dinoflagellate Gymnodinium catenatum is the only known gymnodinioid dinoflagellate that produces paralytic shellfish toxins (PST). Dense blooms caused by the dinoflagellate have been frequently reported in coastal waters of Fujian, China since 2017. While there is still limited understanding of the major physiological characteristics of G. catenatum isolated from Fujian coastal waters, the growth and toxin production of the G. catenatum strain were examined in batch cultures with different levels of irradiance, temperature, salinity, nitrate, and phosphate conditions. The results indicated that the highest maximum cell density of the strain was achieved at 70 µmol m−2 s−1, with the highest growth rate at 120 µmol m−2 s−1. The strain grew well within the temperature range of 15–30 °C, with maximum growth rate and cell density achieved at 20 °C. The dinoflagellate also showed higher tolerance to salinity variation (20–40), with the highest growth rate at salinity 25. Meanwhile, G. catenatum showed higher demand for nitrogen and phosphorus as indicated by its higher half-saturation constant. A decrease in nitrate and phosphate greatly inhibited the growth of G. catenatum. The toxin profile of the G. catenatum strain was conservative and dominated mainly by the N-sulfcarbamoyl C-toxins (> 95%), indicating its hypotoxicity. The cellular toxicity increased with the algal growth, with the highest cellular toxicity observed at the stationary growth phase. The cellular toxicity of G. catenatum also responded to environmental variations including lower temperature (15 °C), lower salinity (20), nitrate-repletion, and phosphate-depletion conditions which enhanced the cellular toxicity, while irradiance exerted non-significant influence. The present study depicted the physiological characteristics of the particular G. catenatum strain and provided valuable insight on the ecophysiology of G. catenatum in natural coastal waters.