The basic difference between a pond and a lake is the depth and the size. A pond is a body of water shallow enough to support rooted plants, with light penetration to the bottom, throughout the pond. Plants will often grow all the way across a shallow pond. Water temperature is fairly even from top to bottom and follows the general trend of the surrounding air temperature; however, the changes in water temperature are not as extreme as in the air. There is little wave action and the bottom is usually covered with sediment. Plants grow along the pond edge. The amount of dissolved oxygen may fluctuate greatly during a day. In very cold climates, the entire pond can freeze solid. The dynamics of a pond are often much more intense than in a lake. A pond has no layers or zones and changes in the environment affect the entire body rather than only one area or section.

A lake is bigger than a pond, and is too deep for light to penetrate to the bottom with enough intensity to support photosynthesis by plants except in shallow areas near the shore. Some lakes are big enough for waves, which can provide needed circulation and oxygen transfer.

During spring and early summer, a lake's surface warms up, and its water separates into layers of different temperatures and densities. As the weather cools in the fall, so do the water temperatures and the layers become mixed until the next spring. Water temperatures in lakes during summer months are not uniform from top to bottom. Three distinct layers develop: The top layer stays warm at around 65-75 degrees F (The middle layer drops dramatically, usually to 45-65 degrees F. The bottom layer is the coldest, staying at around 39-45 degrees F. This is a thermocline or temperature gradient. Thermal stratification, or layers of temperature in water, is more likely in deeper ponds and lakes, or ones without adequate circulation. As the sun shines, the pond surface warms and encourages more plant and algae growth. The cooler, denser water settles to the bottom. This becomes more significant as the summer progresses, and finally there is distinctive layering. The line between the layers is the thermocline. The thermocline acts as a barrier to prevent mixing between the top and bottom of the pond. In the fall, as the water cools, the stratification reverses, and the pond “turns over”, the pond “turns over” again as the water warms in the spring. This turning over can create maintenance problems as sediment and nutrients from the lake bottom is carried into the water column and suspended. This causes both increased turbidity (cloudiness) and additional nutrient for algae growth in the water table. In artificial, man-made lakes, proper circulation and aeration will help prevent stratification and the resulting spring and fall “turn-over“.

The layers in a lake are further categorized into zones defined by both water temperature and light penetration as parts of the overall dynamic ecosystem. The distinction between these classifications often becomes blurred because of the varying conditions in the lake.

This is a brief description of these zones. The littoral zone extends from the shore and the water surface to a depth where light is barely sufficient for rooted plants to grow. The pelagic zone (or "limnetic zone") is the surface water layer in offshore areas beyond the influence of the shoreline. The photic (or "euphotic") zone is the lighted and usually well-mixed portion that extends from the lake surface down to where the light level is reduced to 1% of that at the surface. This depends on the degree of water clarity. The aphotic zone is below the littoral and photic zones extending to the bottom of the lake where light levels are too low for photosynthesis. This deep, unlit region is also known as the profundal zone. The sublittoral zone, which is the deepest area of plant growth, is a transition between the littoral and profundal zones.

Boundaries between these zones vary daily and seasonally with changing sun intensity increase or decrease in water clarity due to algae blooms, sediment inflows, and surface waves. During spring and fall, the lake temperatures are more uniform. Fish and other animals are found throughout the layers of the lake. Even in cold climates, most lakes are large enough so that they don't freeze solid, unlike ponds.
Both lakes and ponds undergo a natural aging process known as eutrophication. They gradually fill in, lakes becoming ponds and ponds becoming marshes, filled with sediment. Eutrophication can be controlled or eliminated by adding additional consumers to the system to control these sediments before they build up. The addition of beneficial microbes to the system can control the sediment buildup, stop the eutrophication process and stabilize the ecosystem.

The maintenance requirements of lakes and ponds runs contrary to their size; very small fish ponds need consistent monitoring, while the ponds on golf courses and other sheltered areas require service only once or twice a week. Larger natural lakes often only get seasonal attention if any at all.