Metabolomic technologies are increasingly being applied to study biological questions in a range of different settings from clinical through to environmental. As with other high-throughput technologies, such as those used in transcriptomics and proteomics, metabolomics continues to generate large volumes of complex data that necessitates computational management. Making sense of this wealth of information also requires access to sufficiently detailed and well annotated meta-data. Here we provide standard reporting requirements for describing biological samples, taken from an environmental context and involved in metabolomic experiments. It is our intention that these reporting requirements should guide and support the standardised annotation, dissemination and interpretation of environmental metabolomics meta-data.