The concentration of heavy metals in sediment is an important factor for assessing the quality of the nearshore environment. Geochemical background values are the normal concentrations of heavy metals in the natural environment. The use of different background values results in different evaluation results. Heavy metal (Cu, Pb, Zn, Cr, Cd, As, and Hg) concentration profiles along a sediment core were investigated to obtain background values and assess the depositional processes and contamination levels in Laizhou Bay. Apart from As and Hg, all other metals had similar distribution patterns and could be divided into four stages since marine isotope stage (MIS) 2. The results of the enrichment factor, geoaccumulation index, Pearson’s correlation coefficient, Nemerow pollution index, principal component analysis, and potential ecological risk index showed that element enrichment or contamination in the core sediments was absent and that all heavy metals were mainly naturally sourced. The changes in heavy metals since MIS 2 in the core sediments were predominantly related to the sedimentary environment, sediment sources, and mean grain size. The average values of the heavy metals in the U2 unit formed during the Middle Holocene can be used as reference values for background values.