Geochemical and environmental-chemical studies based on speciation mainly using X-ray absorption fine structure (XAFS) spectroscopy by the author have been reviewed in this manuscript. These studies revealed that we could understand physico-chemical processes behind the distribution and isotopic data obtained in various geochemical studies by this approach, which can be called as molecular geochemistry. This approach allows us to interpret geochemical cycles of various elements from atomic and molecular scale levels, which in turn enables us (i) to extract more information from geochemical data related to earth history and (ii) to predict environment in future more accurately. The studies introduced here include environmental chemistry of rare earth elements and actinides, behavior of toxic elements at earth surface, environmental impacts of speciation of various elements in aerosols, enrichment of various elements to ferromanganese oxides and its application to paleo-environment studies, understanding of isotope fractionation based on speciation data, and migration of radioactive nuclides emitted by the Fukushima Dai-ichi Nuclear Power Plant accident. It was also shown that development of X-ray spectroscopic methods applied to geochemistry and environmental chemistry has opened new fields in environmental geochemistry and trace element geochemistry. Through these various topics, I would like to emphasize that systematic studies on behavior of various elements in environment in terms of physico-chemical viewpoint can provide various new ideas in wide fields in geochemistry as was suggested by Prof. V. M. Goldschmidt. The basic knowledge of various elements can be a firm basis to use geochemistry to obtain more general information in earth and environmental sciences. The attractiveness and importance of molecular geochemistry indicated in this manuscript suggests that this field can be one of drivers to develop new geochemistry in 21st century.