This paper investigates the mineralogical and geochemical characteristics, as well as the possible sources, of gold, silver, platinum group elements (PGE), copper, and lead found in the beach sands along Egypt’s Mediterranean coast. Using scanning electron microscopy and electron probe micro-analysis, this study determines the morphology and micro-chemistry of separated grains to assess their economic potential and how various minerals respond to different transport distances. The analysis reveals that gold grains are of high purity (94.11 to 98.55 wt.%; average 96 wt.% Au) and are alloyed with Ag (1.28–2.32 wt.%) and Cu (0.16–3.15 wt.%). Two types of gold grains were identified, indicating differences in transport distances. Variations in morphology, surface features, inclusion types, rims, and chemistry of the native metals, including gold grains, suggest differences in composition, weathering degree, transport distance, deposit types, and host rocks. The average Ag concentration in gold grains (1.86 wt.%) suggests a link to mesothermal or supergene deposits. Most silver, copper, and lead grains are spherical, with some variations in shape. Silver grains have 71.66–95.34 wt.% Ag (avg. 82.67 wt.%). Copper grains have 92.54–98.42 wt.% Cu (avg. 94.22 wt.%). Lead grains contain 74.22–84.45 wt.% Pb (avg. 79.26 wt.%). The identified platinum group minerals (PGM) belong to the Pt–Fe alloys and sperrylite, both of which are PPGE-bearing minerals. These metals likely originate from the weathering of upstream Nile tributaries surrounded by igneous and metamorphic rocks from Ethiopian and Central African regions, with a minor contribution from the Egyptian Eastern Desert Mountains.