Chlorophyll fluorescence, a method for noninvasive analysis of the photosynthetic activity in plants and algae, is a commonly used technique in physiology and ecophysiology. In recent years it has developed as a key technique to analyze the regulatory mechanisms of the energy conversion within photosystem II, and is also used as an easy-to-handle indicator of the responses of photosynthetic organisms to environmental changes. The construction of waterproofed instruments for usage in the field facilitates investigations also in the aquatic ecosystems under natural conditions. Although instruments are generally easy to handle it is necessary to understand the theoretical background of this technique and methodology to avoid technical pitfalls as well as misinterpretation of data achieved. Though fluorescence parameters can give hints to the performance of primary production, they are not sufficient for a proper determination. This chapter explains the theoretical and technical background especially for newcomers, explains the most important fluorescence parameters, and introduces and compares the most commonly used instruments that are now available on the market. Moreover, methodological tips for proper measurements are described because operating guidelines of manufacturers are usually insufficient or according to the kind of the measuring protocol special instruments are favored.