In this chapter, we summarize and discuss methods used to study viral interactions in aquatic environments. These methods to assess interactions between viruses, hosts and the environment (including other viruses) are operationally separated into interactions at the molecular, single-cell, and community levels. Many of these methods benefit from the methodological advancements in the field of molecular biology including the 'Omics area'. There are, however, numerous methods from other fields. We also present examples of unanswered questions along with problems solved by these questions. Finally, we conclude that viral interactions with the abiotic environment have received surprisingly little attention, so far, from a methodological perspective.