Exposomic studies of the rapidly changing environment of the Three Gorges Reservoir (TGR) after its impounding is elaborated as a novel field of human and environmental research. Molecular exposomics is focused on the measure of all exposures to molecules and especially persistent organic pollutants-like compounds are of emerging interest due to their lifetime existence in the environment and humans. Theoretical considerations in general and particular for the TGR are deduced and presented using quantitative approaches for this research field. Since exposomics is strongly time-dependent, a theory is presented to link extension of exposure, time, and related effects. Similarity to the first law of thermodynamics is outlined. On top of this, the integrated use of biomarkers is presented employing chemical analysis for biomarkers of exposure and effects, biomarkers in vivo, in vitro approaches and the link between chemical mixtures, and the onset of disease and lethality. Besides real organisms, also virtual organisms are favored to act as well-defined sub-compartments such as fat of biota and with respect to time of exposure. Exposomics is the perspective of risk evaluation and chronic exposures in the running century. It needs novel theories, approaches, and integrated action between medical and environmental disciplines. The existing knowledge about molecular stressors has to be assembled and put into a context especially with respect not only to time resp. lifetime exposure of humans but also eco-toxicological findings by using highly conserved phylogenetic mechanisms to enable links between human and risks of environmental biota. The TGR is a good example not only to employ biomonitoring of real but also virtual organisms due to the lack of established ecotopes in this changing environment so far. Progress in understanding long-term risks requires a proper theory as well as novel tools such as virtual organisms. On top, multidisciplinary approaches and the utilization of existing knowledge about the exposure of the environment and humans have to be merged and directed into mutual concepts. Effect-oriented and chemical analysis must be designed time-oriented to determine lifetime exposures of mankind and nature. Perspectively, a first attempt about exposomic theory and concepts is proposed and has to be developed experimentally further enclosing virtual besides of real organisms and compartments. Environmental and human exposomics have to be considered as a unified global issue in order to effectively utilize their mutual existing knowledge most effectively. The TGR is a challenging model system aiming this objective.