The lake or ocean is a very patchy structure and this may allow for the diversity. Also there are other pressures on the algal populations, not the least of which is grazing by zooplankton and phytophagous fish. Not only do algae have to contend with herbivores but also parasites of the fungal type . In addition, there is the problem with light levels. There is a compensation point also referred to as the compensation depth that differs with different species.
Pigmentation allows for a difference in the compensation depth.
This is due in part to the difference in water temperature and related water density. During this period the nutrients circulate within the respective strata. The thermocline is thinner than the diagram and remains as a barrier. During the winter months in lakes in North America, the waters are generally homeothermic. The circulation pattern is from top to bottom.