During the summer months, as the water warms, there will be a warm layer of water, and a cold layer of water, with a third layer sandwiched in-between called the thermocline. Accordingly, in this middle layer, the temperature of the water decreases dramatically about 1-degree C., for each meter of depth. The dissolved oxygen content contained in each layer also differs dramatically.
The warmer and colder layers may contain dissolved oxygen levels that are poorly oxygenated, while the thermocline will be oxygen rich (in most lakes), and thus more attractive to various species of fish. You will no doubt recall various stories youve read whereby the professional fishermen have stated they found the thermocline at such and such a depth and the fish were hitting like crazy.
As fall approaches, and the nights become cooler, wind and wave action aid in lowering the surface temperature of the water, and just like cold air is heavier than warm air, the now cooler surface water drops down through the warmer water. As the warmer water rises, it also brings with it nutrients and suspended sediment, which are added to the dying and decaying plant matter created by the approach of fall. As a result, the water temperature, and more importantly for the fish, the dissolved oxygen content of the water is close to being the same at all depths, thus species of fish that were once restricted all summer to areas of the thermocline where oxygen was plentiful, they are now free to roam the entire lake.
When this occurs, you end up with stained looking water. With regard to fishing, this is a good thing. Look for the areas that have sharp contrasts in water color, and you will find bass. Look for the same area and "cover," and you will find concentrations of bass.
Although the above explanation is an aggregate of scientific principles, someone once asked, "How will I recognize when this occurs?" The answer to this question is not scientific at all. With enough time on the water during this transition period, your nose will inform you when this annual event has occurred. You can smell it.