The presence of roads, farm house foundations, wells and Liangzhu period cultural relics in the bottom of Lake Taihu attest to the fact that this shallow depression was probably dry between 4 and 5 thousand years ago. This interpretation is corroborated by the sudden disappearance of algal pigments at sediment depths carbon-14 dated at 4-5 thousand years before present.
In winter, the stronger winds are predominantly from the northeast. These winds result in a powerful counterclockwise current that transports lake sediments and has altered the very shape of the lake over the last 300 years. Winds produce a complex mixing pattern in Lake Taihu with storm induced sediment deposition occurring near the lake's center.
During approximately 240 days of the year, the wind blows across Lake Taihu with sufficient force to mix it to its bottom. As a result, this polymictic lake rarely becomes anoxic and dissolved oxygen at the mud water interface is maintained at or above 4 mg·l^-1. The consequences of this high dissolved oxygen are quite impressive as high organic loading to the lake would otherwise render its bottom waters anaerobic killing many of its natural inhabitants.
Because suspended solids reduce (attenuate) light penetration, the major primary production takes place in the top metre of the lake (mean Secchi Transparency-0.25 m). Suspended clays are slow to settle and wind mixing keeps fine-grained suspended solids in suspension in all but the most quiet backwaters of the lake.
In the recent past about 23 000 metric tonnes of phytoplankton were produced in Lake Taihu. This large production represents only about 5% of the total influx of organic material entering the lake. In summer and fall, cyanobacteria such as Microcystis spp. and Anabaena spp. dominate most of the lake. Recently, however, mixotrophic flagellates displaced cyanobacteria as the dominant algae in parts of Lake Taihu with high bacteria and high suspended solids (e.g. Wuli and Meiliang Bay). In the future, facultative heterotrophs may come to dominate an ever larger portion of the lake waterc column.