Hydroprocessing facilities may operate for extended periods of time before detection of mercury in the inlet facilities, as mercury adsorbs onto the metallic pipelines used to transport the hydrocarbon fluids, e.g., gas, produced waters, from the wells to processing facilities (“flowlines”). Once the pipelines become “saturated” with mercury, mercury will breakthrough and be detected at the inlet facilities. A mercury management/control scheme is disclosed wherein a chemical treatment step using aqueous sulfidic solution is integrated into a progressive pigging plan to clean the pipeline, managing mercury accumulation in the pipeline for a reduced mercury concentration in the fluid exiting the flowlines.