Mechanisms of PPR and macromolecular conformation changes that control the efficiency of energy transduction in photosynthesis are discussed.Special attention is focused on the analysis of chlorophyll fluorescence as an integrated parameter indicative of efficiency of light energy accumulation and cell state.Using mathematical and computer modeling of primary processes of photosynthesis the multicomponent models are introduced.This generalized kinetic model give a clear picture of the interaction of components of the electron transport chain in the photosynthetic membrane.The combination of different methods of description (differential equations and formalism of Brown dynamics) allows one model the processes in complex three-dimensional interior of a vegetative cell that collectively provide a high efficiency of energy transformation in photosynthesis.Sharp changes in environmental conditions as well as other unfavorable factors may lead to the distortions of the coupling between consecutive electron transfer steps and to the generation of active oxygen forms responsible for the subsequent oxidative stress.The results are presented on the actual elaboration of the express diagnostics methods and apparatus for ecological monitoring of water bodies.