<p>The original formulation of the conceptual model of a high-rate algal pond (HRAP) treating wastewater was represented as a black box with two inputs (organic waste and solar energy) and two outputs (biomass and treated wastewater). Bacterial oxidation and algal photosynthesis are the two services that provide wastewater processing capabilities. The conceptual model, referred to here as HRAPv1, has enabled the establishment of HRAPs for the efficient treatment of a variety of wastewaters, producing safe water and useful biomass. In the almost 70 intervening years, much has been learned about the HRAP microbial and eukaryotic communities, which produce microalgal biofuel feedstock, or render safe chemicals of emerging concern. However, the viral community associated with HRAP has received sparse consideration in the literature. Viruses have an all-pervading, global distribution, significantly affecting all biogeochemical cycling and we suggest similar activity is occurring in HRAPs. Here, we briefly consider the role of microalgae in the treatment of wastewater, with emphasis on HRAPs and acknowledge that the microalgae are accompanied by bacteria, archaea, micro-eukaryote and virus consorts that combine to provide a practical treatment system. Given the absence of significant numbers of publications on the viral ecology of HRAPs we provide a perspective on the potential influence of DNA viruses on the ecology of HRAPs by analogy with other aquatic systems. An array of multi-omics technologies is available, revealing new phyla, such as nucleocytoplasmic large DNA viruses (NCLDVs), and many offensive and defensive strategies used by both the viruses and their hosts. We highlight the relationship of these companions with the microalgae and describe a new conceptual model (HRAPv2) of the dynamic, multi-domain interactions potentially shaping the HRAP community, which are worthy of further research.</p>