This study investigated the feasibility of embedding two low-energy dilution desalination processes, namely osmotic dilution desalination (ODD; the FO-RO membrane configuration) and mixing dilution desalination (MDD; the UF-RO membrane configuration), in a conventional seawater desalination approach (i.e., seawater reverse osmosis) using real seawater and recycled wastewater. The removal efficacy of bacterial indicators (Clostridium perfringens and Escherichia coli), coliphage genera Microviradae, and Human adenovirus (HAdV) was assessed in influent/effluent samples collected from each membrane configuration. Mixing dilution of the influent feed waters reduced the number of all pathogenic contaminants as well as organic/inorganic compounds. The rejection rate of total suspended solids was 35.7% in FO to 63.6% in UF respectively, whereas that of total organic carbon was 53.8% and 56.9% in FO and UF, respectively. The FO membrane in the ODD process more efficiently removed viruses (5.0 LRV) and bacterial indicators (4.2 LRV) than the UF membrane (3.7 and 3.6 LRV, respectively). Nevertheless, the different methods of detection used in our study, such as culture-based and qPCR, were found to have significant influences on the LRVs. Comparative 16S rRNA sequencing indicated that the vast majority of bacterial indicators in RO permeating from the FO-RO and UF-RO configurations were nonpathogenic strains.