Environmental DNA (eDNA) is often used as a template for metabarcoding, but eDNA can be detected from deceased organisms or organisms no longer present in the environment during the sampling period. Environmental RNA (eRNA) can also be used in downstream metabarcoding applications with the key benefits that RNA is produced by living organisms and may degrade faster in aquatic environments compared to DNA. Therefore, eRNA has the potential to be the favorable metabarcoding template for experiments where detection of primarily living organisms or sampling time is critical, such as in ecotoxicology assays. Few studies have explored the usefulness of eDNA compared to eRNA in different environments. It is useful to investigate the differences between communities detected from each type of nucleic acid to further develop eRNA as a molecular ecology tool. The study goals are to 1) compare the utility of eRNA and eDNA for metabarcoding of benthic estuarine samples and 2) use a metabarcoding approach to investigate the effects of emerging contaminants on benthic eukaryotic and prokaryotic community diversity.