Trace elements contamination and accumulation in bottom sediment represents a risk to environment and aquatic biota. Their anthropogenic or natural discharge, extension and cumulation can cause large scale of ecological destructions. Bioaccumulation and biomagnification is capable of leading to toxic level of these chemical substances in fish and other fresh water organisms (benthos, zooplankton), even when the exposure is low. The fish contamination through trophic structure can cause serious consequences to human health. The aim of the manuscript was to assemble and summarize the latest literature on the environmental and the aquatic biota effects of trace element contamination of bottom sediments. The article is also a review of new methods for trace elements elimination and their assessment to impact on aquatic organisms . Based on collected scientific publications in last 20 years the most common and important trace elements in aquatic ecosystem are Chromium, Arsenic, Mercury, Cadmium and Copper. These compounds are dangerous for living organisms and can disrupt their homeostasis as well as a cardiovascular, nervous and digestive system. Nowadays exist many instrumental methods, which are available to determine the trace element concentration such as PMF, INNA, BCR, XRF and bioassay. In searched studies the most preferred and used analyse of trace element concentration in aquatic bottom sediments is bioassay. This biological method is good complement to physical and chemical analyses in procedures of sediment quality assessment. Bioassay method can indicate sensitive response of planktonic organisms to various trace elements and provide information about the real risk to aquatic life.