The main problem is that the explosive growth of the phytoplankton rapidly depletes the available nutrients. With the nutrient supply on the wane, the productivity of the phytoplankton decreases. Many of the phytoplankton cells die and begin to sink to the bottom. At the same time, the increasing water temperatures begin to cause a boundary to form between warm surface waters and deeper cold waters. This boundary is called the thermocline, and the condition where there are defined layers in the water column is stratification.
Stratification is a typical summer condition in many bodies of water.
Under stratified conditions, remineralized nutrients in the deeper cold water can't reach the surface waters, where the light is strongest. Furthermore, the concentration of dissolved gases in the water, particularly oxygen, decreases, due both to higher temperatures and the respiration of organic matter by bacteria. The pattern of events in the fall is initiated by decreasing air temperatures. The temperature of the water at the surface decreases, to a point where the surface waters are cooler than the deeper water. Because warm water rises, the water column is unstable.