As fall progresses towards winter, the surface cools and the lake again becomes isothermal. This time, however, the temperature is higher than the point of maximum density (4°C), though not by much. The surface water continues to cool, it becomes more dense than the water on the bottom, and then the lake turns over rapidly. In just a few days nutrient-rich but oxygen-starved water on the bottom is exchanged with water on the top having opposite composition. The lake becomes turbid as bottom sediments rise with the current. Continued cooling leads again to thermal stratification, but this time with colder water on the surface. Further cooling results in ice.

Of course the nutrient/thermal cycle does not take place exactly as described. In a lake with as many coves as Squam, broken up by many reefs and islands, the processes described above happen at different times in different locations. Because the water is so clear, sunlight warms more than just the surface, making the boundaries of the layers somewhat indistinct. Along the shore, nutrients enter the epilimnion from drainage or seepage. In shallow coves, nutrients from bottom sediments can reach the surface, especially if they are stirred up by strong wave action or by propellers. In fact, clear stratification has been measured only over deep water. Imperfect as the model is, it is useful in understanding the annual changes that take place in the lake.

One of SLA's most important functions during the summer is to support the NH Lay Lakes Monitoring Program run by the University of New Hampshire. Now in its 20th year, the results help identify long-term trends in water quality.

Monitoring to date has documented a very gradual decline in water quality, but Squam Lake remains an unproductive or 'oligotrophic' lake. Little Squam, the shores of which are more developed, is at risk of becoming a productive or 'eutrophic' lake. Such lakes often have reduced clarity caused by algae blooms.

The last ice on Squam has usually melted by the last week of April. Other phases of the annual thermal cycle can also be seen or measured, but that part relating to ice is the most easily recognized. In the winter, the top of the lake is colder than the bottom because the density of water is greatest at 4°C. Anything warmer or colder rises, so the bottom of the lake in winter is nearly always 4°C, even though there is ice on the surface.

When surface water warms to 4°C, the temperature of the lake becomes uniform (isothermal). Under such conditions, very little energy is needed to stir up the water, and the wind easily supplies it. For several days in the early spring, oxygen-rich surface water mixes with nutrient-rich water on the bottom. Turbidity increases as this takes place.

Vertical circulation in the lake stops as the surface warms. The water becomes thermally stratified, with a nearly uniform upper layer (the epilimnion) of warm water that reaches a temperature of 22-24°C and a depth of 15-20 feet by mid-summer. Below it lies a layer (the metalimnion) typically three feet deep in which the temperature drops sharply with depth. The bottom layer (the hypolimnion) remains cold, about 6-8°C.

When the lake becomes stratified thermally, it also becomes stratified chemically. Near the surface, the concentration of dissolved oxygen remains high, but the amounts of nitrogen and phosphorus compounds decrease as plants use up nutrients. Dead organic matter sinks. Decomposition of bottom sediments and respiration of deep water organisms in the hypolimnion use up dissolved oxygen. The amount of dissolved carbon dioxide and the level of acidity rise. The changing chemical balance may threaten the survival of fish who need the cold water.