This paper provides an overview of different methods of assessing the trace metal (TM) contamination status of sediments affected by anthropogenic interference. The geochemical background determination methods are also described. A total of 25 papers covering rivers, lakes, and retention tanks sediments in areas subjected to anthropogenic pressure from the last three years (2019, 2020, and 2021) were analysed to support our examination of the assessment measures. Geochemical and ecotoxicological classifications are presented that may prove useful for sediment evaluation. Among the geochemical indices, several individual pollution indices (CF, Igeo, EF, Pi (SPI), PTT), complex pollution indices (PLI, Cdeg, mCdeg, Pisum, PIAvg, PIaAvg, PIN, PIProd, PIapProd, PIvectorM, PINemerow, IntPI, MPI), and geochemical classifications are compared. The ecotoxicological assessment includes an overview of Sediment Quality Guidelines (SQG) and classifications introduced nationally (as LAWA or modified LAWA). The ecotoxicological indices presented in this review cover individual (ERi) and complex indices (CSI, SPI, RAC, PERI, MERMQ). Biomonitoring of contaminated sites based on plant bioindicators is extensively explored as an indirect method for evaluating pollution sites. The most commonly used indices in the reviewed papers were Igeo, EF, and CF. Many authors referred to ecotoxicological assessment via SQG. Moreover, PERI, which includes the toxic response index, was just as popular. The most recognised bioindicators include the Phragmites and Salix species. Phragmites can be considered for Fe, Cu, Cd, and Ni bioindication in sites, while Salix hybrid cultivars such as Klara may be considered for phytostabilisation and rhizofiltration due to higher Cu, Zn, and Ni accumulation in roots. Vetiveria zizanoides demonstrated resistance to As stress and feasibility for the remediation of As. Moreover, bioindicators offer a feasible tool for recovering valuable elements for the development of a circular economy (e.g., rare earth elements).