All animals and many bacteria use oxygen and release carbon dioxide

Carbon dioxide is an odorless, colorless gas produced during the respiration cycle of animals, plants and bacteria. All animals and many bacteria use oxygen and release carbon dioxide. Green plants, in turn, absorb the carbon dioxide and, by the process of photosynthesis, produce oxygen and carbon-rich foods. The general formulas for plant photosynthesis and respiration are summarized below.
Photosynthesis (in the presence of light and chlorophyll):

Carbon dioxide	+	Water	à	Oxygen	+	Carbon-rich foods
CO2		H2O		O2		C6H12O6

Respiration:
+ Oxygen à Carbon dioxide + Water

Carbon-rich foods	+	Oxygen	à	Carbon Dioxide	+	Water
C6H12O6		O2		CO2		H2O

Green plants carry on photosynthesis only in the presence of light. At night, they respire and burn the food they made during the day. Consequently, more oxygen is used and more carbon dioxide enters waterways at night than during the daytime. When carbon dioxide levels are high and oxygen levels are low, fish have trouble respiring (taking up oxygen), and their problems become worse as water temperatures rise. As you can see from the table, even small amounts of carbon dioxide can affect fish.
It’s lucky for fish that "free" carbon dioxide (by "free" we mean it is not combined with anything) levels rarely exceed 20 mg/L (milligrams per liter), because most fish are able to tolerate this carbon dioxide level without bad effects.
When several days of heavy cloud cover occur, plants’ ability to photosynthesize is reduced. When that happens in a pond containing lots of plant life, fish can be hurt in two ways: by low dissolved oxygen and by high carbon dioxide levels.
Carbon dioxide quickly combines in water to form carbonic acid, a weak acid. The presence of carbonic acid in waterways may be good or bad depending on the water’s pH and alkalinity. If the water is alkaline (high pH), the carbonic acid will act to neutralize it. But if the water is already quite acid (low pH), the carbonic acid will only make things worse by making it even more acid.

Table 2. Effects of CO2 on fish
CO2 (in mg/L)	Effect
1.0-6.0	Fish avoid these waters.
12	Few fresh-water fish can survive for long periods of time in water with a carbon dioxide level greater than this.
30	Kills the most sensitive fish immediately.
45	Maximum limit for trout
Above 50	Trout eggs won’t hatch.