Wadi Maryut Lake is one of the remaining parts of the ancient Lake Mareotis and is not mentioned in the scientific literature. For the first time, physical and chemical characteristics as well as elemental concentrations in sediment, water, soil, and plants were determined. The lowest metal pollution indices are in the northeastern end of the lake and tend to increase toward the other end. In lake aquatic environment, Al, Fe, K, Mn, Na, B, and Cr are more likely to exist in insoluble form in the southwestern part and in soluble form in the northeastern part. Using different approaches to assess sediment contamination demonstrates that sediments can be categorized as unpolluted. However, the geo-accumulation index suggests that two locations have low anthropogenic influence of Pb and the enrichment factors and the degree of contamination indicate that Co and Pb may be enriched in sediment of some locations. Comparisons with consensus-based sediment quality guidelines revealed that no sample exceeded the probable effect concentration for Cr, Cu, Ni, Pb, and Zn. The most mobile elements in sediment-water and soil-plant systems are Na, K, and Pb. In sediment-water system, Al, Fe, and Mn oxides have the major influence on scavenging of B, K, and Cr. Similarity in the occurrences of Mn, K, and Fe in soil and Mn and Fe in wild plant was found. This work demonstrates the state of decontamination of the lake and confirms its importance as a reference and comparative case for south Mediterranean coastal water bodies.