Environmental RNA (eRNA) analysis has emerged as a promising tool for assessing the physiological status of macro-organisms in aquatic environments. However, existing eRNA analysis for physiological assessments has been limited to laboratory experiments. To explore the potential of eRNA under non-laboratory conditions, this study re-analyzed two published metatranscriptome datasets from an aquaculture facility and an aquarium. The re-analysis revealed that functional genes, such as tlr4, lrp12, and elovl1, were detected as eRNA from Pacific oyster (Magallana gigas), whale shark (Rhincodon typus), zebra shark (Stegostoma tigrinum), and green sea turtle (Chelonia mydas). This result highlights the feasibility of using eRNA to assess biological processes, including immune responses and fatty acid metabolism. Despite these successes, challenges such as the dominance of microbial RNA, low sequencing depth, and RNA degradation were identified. Strategies to overcome these challenges were discussed as pathways for advancing eRNA analysis. This study provides a foundational direction for developing eRNA analysis as a non-invasive tool for ecological monitoring and the management of aquatic organisms in non-laboratory environments.