Ballast water is one of the most important vectors for transferring and spreading marine aquatic species throughout the world. While technological advancements have led to an enhanced comprehension of ballast water viromes, the understanding of viral diversity in the residues after deballasting such as sediment and residual water remains predominantly unexplored. Our research conducted an initial exploration of viromes present in both residues (sediment and residual water) and ballast water of ballast tanks at Shanghai port, revealing distinct profiles between viromes in sediment and the water column (residual water and ballast water). The diversity, richness, and evenness of viral communities in sediment were lower than those in the water column. Our study underscores the existence of viral pathogens within residues and ballast water. Shrimp hemocyte iridescent virus (SHIV), a strain of decapod iridescent virus 1 (DIV1) listed as an aquatic animal disease by the World Organization for Animal Health (WOAH), was identified in all three types of samples. Our research expanded the understanding of viral diversity in sediments and residual water, highlighting the need for better management of residues after deballsting.