Mass cultivation of the chlorophyte Chaetomorpha crassa has the potential to serve as a biological filter for the reduction of eutrophication in summertime Japanese waters. In order to clarify the suitability of C. crassa for this purpose, seasonal changes in its photosynthesis, growth, NO3–N uptake, nitrogen content, and salinity tolerance were investigated trimonthly from May 2011 to February 2012, with samples collected in Nagatsuraura Lagoon, northern Japan. Significant effects of seawater temperature on photosynthesis, growth, and nitrogen accumulation were also detected in all four seasons, and all parameters at summer temperatures (24–28 °C) were significantly greater than those at the temperatures of other seasons (8–20 °C). Moreover, compared to the other three seasons, C. crassa showed significantly higher growth rates at 16–4 psu and higher survival percentages at 8–2 psu during the summer. In conclusion, due to its high capacity for growth and nitrogen accumulation, and greater physiological tolerance of low salinity during the elevated temperature period, large-scale cultivation of C. crassa could play a significant role in the bioremediation of both saline and brackish waters during summer.