Although the phytoplankton and protozoan assemblages of Lake Winnipeg are quite variable both, spatial and temporally, knowledge of their current distribution and ecology enables them to be used as indicators providing unique information concerning past and recent ecosystem conditions. Many of the main taxa have been similar throughout history although there have been dramatic changes in their abundance. Lake Winnipeg is currently very responsive to the climatic conditions in its drainage basin and it appears, historically, to have been a diatom-bluegreen algal lake with Tintinnids and thecate amoeba forming significant components of the protozoan community. A wide variety of microfossil remains have been used to infer past conditions in this large prairie lake.
Microfossils reported from the long core 103 (8 m) taken from the north basin of LakeWinnipeg and short core Namao 7a taken from the south basin of the lake in August 1994 indicate that the lake has experienced several changes over its history. Diatom assemblages, low throughout the core 103 below 50 cm, except for a peak around 300–400 cm are virtually absent below 690–800 cm (Lake Agassiz). Stephanodiscus and Aulacoseira are the two major pelagic diatom genera represented throughout the lake's history. Species changes occur near the top of the core indicate increased anthropogenic eutrophication. Shallow water littoral taxa were never abundant at either coring sites. The presence of planktic cyanoprokaryote (cyanophyte, cyanobacteria, bluegreen algae) remains (akinetes) from 600 cm depth and the progressive increase in abundance from 400 cm to through the top 100 cm of the core indicates increasing phosphorus levels, warming summer temperatures and increasing summer nitrogen limitation in the lake. Nitrogen fixing bluegreens (especially Anabaena and Aphanizomenon akinetes) and the diatoms (Aulacoseira ambigua, A. granulata, A. islandica, S. binderanus, and S. niagarae) were abundant in the upper sediments and changes after 100 cm can be interpreted as the effects of human impact. These taxa indicative of increase eutrophication, in addition to S. agassizensis, Melosira varians and Cyclostephanos dubius, are representative of present day plankton.
The short core Namao 7a was dated by Pb210 and the fossil remains also show a rise in the Aulacoseira (particularly A. granulata and A. ambigua) and bluegreen akinetes in the last 40 years as was seen in the upper sediments of the 103 core. There was an interesting peak in chrysophyte cysts during the 1930's which corresponds nicely with climatic conditions during this period. The fires accompaning the hot dry period in the mid 70's can be seen in the dramatic rise in charcoal during this period. Multiple types of micro fossils remains provides several useful tools for interpreting past lacustrine conditions.