Nucleic acids (DNA and RNA) store and express the genetic code for all living organisms, and sampling these molecules after they are shed into the environment allows us to efficiently explore the distribution of aquatic species. While uncertainties remain in interpreting environmental DNA (eDNA) data, even less is known about environmental RNA (eRNA). Researchers initially assumed eRNA was too unstable to persist in water samples, but recent studies suggest eRNA can be abundant in aquatic environments. Further, the inherent instability of RNA molecules may yield more precise information from eRNA samples than eDNA samples. However, the volatility of eRNA also brings unique methodological challenges, making it unclear whether eDNA protocols are suitable for eRNA samples. To address this gap, we compared various methods for preserving and extracting eRNA from water samples using naturally-occurring eRNA and eDNA from Largemouth Bass (Micropterus salmoides) as well as DNA and RNA extracted from Bluegill (Lepomis megalotis) tissues. While working with eRNA presented both expected and unexpected challenges, these difficulties ultimately generated a deeper understanding of the methodology necessary to advance eRNA applications. We found that methods developed for eDNA samples can be readily repurposed and successfully applied to preserve and process eRNA with minimal modifications. For example, we found refrigeration of water samples to be an effective method for short-term preservation of eRNA in the field, with water samples on ice in a cooler showing minimal eRNA degradation over 25 hours. We also found that a low-cost chloroform extraction protocol yielded comparable eRNA quantities relative to much more expensive commercial kits, in some cases even outperforming these methods. Overall, this work demonstrates the practical feasibility of eRNA sampling and provides foundational best practices for future work on eRNA in natural ecosystems.