Traditional environmental biomonitoring approaches have limitations in terms of species detectability and their capacity to account for spatial and temporal variation. Furthermore, as invasive techniques they can be harmful to individual organisms, populations and habitats. The application of non-invasive sampling methods that extract, isolate and identify nucleic acid sequences (i.e. DNA, RNA) from environmental matrices have significant potential for complementing, or even ultimately replacing, current methods of biological environmental assessment. These environmental DNA (eDNA) and environmental RNA (eRNA) techniques increase spatial and temporal acuity of monitoring, and in the case of the latter, may provide functional information regarding the health of individuals, and thus ecosystems. However, these assessments require robust analysis of factors such as the detectability and specificity of the developed assays. The presented work highlights the current and future uses of nucleic acid-based biomonitoring regimes, with a focus on fish and aquatic invertebrates and their utility for water quality, biodiversity and species-specific monitoring. These techniques are compared to traditional approaches, with a particular emphasis on the potential insights that could be provided by eRNA analysis, including the benefits of microRNAs as assay targets.