Carbon dioxide is an important gas in lakes. Although highly soluble in water, most carbon dixide in lakes is formed as an end product of respiration. As carbon dioxide dissolves in water, it form a series of compounds, including carbonic acid, bicarbonate and carbonate. The resulting carbonate chemistry, along with common anions such as hydroxide (OH-) and sulfate (SO4-), contribute to the alkalinity (buffering capacity) of water. Alkalinity is a measure of the ability of water to resist changes in PH, which is a measure of the amount of acidity. A neutral pH is 7; acidic conditions have pH less than 7; and alkaline solution have pH greater than 7.
Many aquatic organisms have fairly strict pH requirements, so the amount and stability of pH is very important. For example, the poorly buffered lakes they are unable to resist changes in pH caused by acidic precipitation, and the resulting low pH values (<5.5) reduced the diversity of organisms to only those few adapted to low pH.
Alkalinity is a conservative parameter which means it does not change readily in well-buffered lakes. On the other hand, pH values may vary both temporally and spatially with in a lake. During intense photosynthesis in the euphotic zone, carbon dioxide and carbonic acid can become less abundant. With less of this acid, pH values may rise to as high as 9. Additionally, respiration in the hypolimnion of a productive lake produces an excess of carbon dioxide, which dissociates to carbonic acid and lowers the pH.
Although lake sediments serve as an ultimate sink for whatever is in the water, movement of materials is not solely to the sediments. Storng storms and turnover events may mix sediment to be eventually mixed into the surface waters by internal currents or during periods of turnover. The chemical enviironment in the sediments is dynamic. Biological and chemical processes continually bring change. When dead plant material settles onto the sediment, bacterial decomposers use this organic matter as food and convert the organic phosphorus to phosphate and the organic nitrogen to ammonia. If oxygen is present, ammonia can be oxidized to nitrate, and oxidized iron can tie up the phospate as ferric phosphate. However, if reducing conditions occur, the nitrate is reduced back to ammonia, and the ferric iron is reduced to ferrous iron, which cannot hold the phosphate. Phosphate is then released back into the water. This reaction is referred to as "internal phosphorus loading" and is a major source of phosphorus to eutrophic lakes.