If you polled people with a lot of lake assessment experience about what technique provides the most information for the money, chances are that Secchi disk transparency would be the choice, but temperature and oxygen profiles would get at least an honorable mention. The thermal structure of a lake is extremely important to the oxygen regime, which is critical to so many aspects of water quality and lake ecology. Temperature and oxygen profiles collected over the course of the year provide extremely valuable data for understanding your lake.
One needs an instrument that measures temperature and oxygen in water to collect these profiles, and a number of high quality instruments are on the market. YSI and Hach have the biggest market share, but there are others worth considering. Bear in mind that you get what you pay for. Temperature is based on differential movement of metals that respond to temperature change and instruments cannot be calibrated by users; one needs to check against a thermometer or known temperature once in a while, but temperature measures are generally reliable. Oxygen used to be done as a titration in lab or field, then moved to instruments with membranes that measured potential across that boundary, and now are done with luminescence, although all three approaches are still in use. Calibration is essential but not difficult for instruments.
A long enough cable is needed to reach the bottom from the boat or dock, and measurements are typically made every half meter (shallow lakes) to every 3 meters (very deep lakes), with 1 meter intervals most common. If the lake is deep enough to stratify, there will be a transition zone between upper and lower water layers and the thickness of that transition zone may be of interest, so more frequent measures (shorter vertical distance between readings) may be advisable near that boundary, called the metalimnion (with the point of inflection for temperature change called the thermocline). It is also important to get readings near the bottom, or even right in the sediment. Certainly the deepest reading should be no more than a few inches from the bottom, and you may find that oxygen declines sharply as the probe hits the sediment.
Graphing temperature and oxygen profiles provides a useful visual image of what is going on (Figure 1), and the pattern over time can be put on the same graph for comparison (Figure 2). Even shallow lakes may exhibit a decline in temperature, and a difference of only 3 Co can be enough to resist mixing. Even without a discernible change in temperature, there can be oxygen depression or even depletion near the bottom if the oxygen demand is high enough; oxygen doesn’t diffuse all that fast through water, and decay can outpace re-aeration.
So why are these profiles important? Higher temperatures increase metabolism and limit the types of organisms that can be present, perhaps most notably fish; trout do not do well at temperatures much above 21oC. The temperature structure of the lake tells us about how much mixing is going on over space and time, and in the absence of adequate mixing, oxygen loss can occur. Loss of oxygen affects nearly all biological components of a lake; sensitive species cannot tolerate oxygen much less than 5 mg/L, few aerobic organisms do well at oxygen <2 mg/L, conversion of ammonium to nitrate ceases when oxygen runs out, and release of iron-bound phosphorus can occur at low oxygen concentrations. Much can be predicted about the status of a lake from temperature and oxygen profiles.