Trace metals and their species in sediments are powerful proxies to indicate the human induced environmental changes of waters including heavy metal contamination, primary productivity and redox conditions of depositional environment. Concentrations of heavy metals in sediments from many waters have substantially increased over the past century. This revealed the elevated loading of heavy metals caused by various human activities, such as mining, smelting, sewage discharge, application of fertilizer and the combustion of coal and oil, etc. Cu, Zn, Ni, Ba and Cd are micro nutrients for phytoplankton, whose concentrations in sediments could indicate the changes in primary productivity in water. Redox sensitive elements including U, Mo, V, Cu, Cd and Mn and their ratios, such as Re/Mo, Cd/U, Th/U and V/Sc, were useful tracers for redox state of the depositional environment. It is worth noticing that these productivity and redox proxies could hardly reflect the productivity and redox conditions in waters which were strongly affected by human activities. This probably results from the anthropogenic input of these elements which might mask their authigenic and diagenetic records in sediment. Therefore, identification of the sources of trace metals is crucial in indicating past environmental changes. Several chemical and statistical methods for discriminating the sources of trace metals have been summarized, including isotopic tracer, chemical extraction, enrichment factor and principal factor analysis. Furthermore, digenesis might disturb the sediment records of trace metals and thus affect the reconstruction of environment changes of water by these metals. The application of multiple metal proxies is a promising way to properly read the sediment records and reconstruct the history of aquatic environmental changes.