Leaf gas exchange is central to the analysis of photosynthetic processes and the development of more productive, water efficient and stress tolerant crops. This has led to a rapid expansion in the use of commercial plant photosynthesis systems which combine infra-red gas analysis and chlorophyll fluorescence (Chl-Flr) capabilities. The present review provides an introduction to the principles, common sources of error, basic measurements and protocols when using these plant photosynthesis systems. We summarise techniques to characterise the physiology of light harvesting, photosynthetic capacity and rates of respiration in the light and dark. The underlying concepts and calculation of mesophyll conductance of CO2 from the intercellular air-space to the carboxylation site within chloroplasts using leaf gas exchange and Chl-Flr are introduced. The analysis of stomatal kinetic responses is also presented, and its significance in terms of stomatal physiological control of photosynthesis that determines plant carbon and water efficiency in response to short-term variations in environmental conditions. These techniques can be utilised in the identification of the irrigation technique most suited to a particular crop, scheduling of water application in precision irrigation, and phenotyping of crops for growth under conditions of drought, temperature extremes, elevated [CO2] or exposure to pollutants.