Heavy metal abundance and potential environmental risks are reported for surface sediments (n = 21) from the Port of Koper area, Republic of Slovenia. The enrichment factor (EF) indicates minor enrichment in arsenic (As), cadmium (Cd), copper (Cu), molybdenum (Mo), lead (Pb), antimony (Sb), and zinc (Zn), moderately to severely enriched with nickel (Ni). The trace metal chemistries, in the context of sediment quality guidelines (SQG), imply adverse threshold effect concentrations (TEC) and probable effect concentrations (PEC), for Ni only. Sediment sequential leaching experiments demonstrated that the majority of heavy metals were of natural lithogenic origin and low bioavailability. The heavy metals’ potential for “Risk Assessment Code” values exhibited no or low anthropogenic environmental burden, with the exception of Mo.