Background metal concentrations are important in assessing pollution level of marine sediments; however, they can be significantly altered by local depositional environments, resulting in significant errors in regional pollution assessment. This study was based on the investigation of the background levels of heavy metals in the Bohai Sea sediments using sediment core, 2-sigma outlier, and regression methods. We also estimate the ecological risks of heavy metals for surface sediments collected from the Bohai Sea using the three methods mentioned above. Ecological risks of heavy metals calculated using the regression method show wide disparities and significant differences from those calculated using the sediment core and 2-sigma methods, indicating that the regression method is not suitable for the Bohai Sea, likely as a result of its complex sources. Conversely, the estimated ecological risks using the sediment core method are moderate, and most heavy metals, except for Hg and Cd, have negligible contamination.