Most of the Třeboňsko PLA belongs to the mildly warm and mildly moist climate zones, with a mild winter. The mean annual temperature in the town of Třeboň, in the middle of the area, is 7.8 °C, with January the coldest month at - 2.8°C and July the warmest at 18 °C.
The average temperature during the vegetative period (April - September) is 14 °C. The mean annual precipitation is 570 mm, with most rain falling in July during summer storms. The snow, having a long-term average of 20 cm depth, usually lays on the ground for 50 - 60 days per year.
The average yearly sunshine total is around 1750 hours per year, with a maximum of 240 hours in June. The relative humidity of the air is very high due to the large proportion of water surfaces and only in the summer months does the daily average fall below 75 %.