This dataset is from a paper which reports on a bibliometric analysis of environmental sciences research in northern Australia between 2000 and 2011. It draws on publications data for Charles Darwin University (CDU) and James Cook University (JCU) researchers to present a bibliometric profile of the journals in which they publish, the citations to their research outputs, and the key research topics discussed in the publications. Framing this analysis, the study explored the relationship between the two universities’ publications and their ‘fit’ with the environmental sciences field as defined by the Australian research assessment model, Excellence in Research for Australia (ERA). The Scopus database retrieved more records than Web of Science, although only minor differences were seen in the journals in which researchers published most frequently and the most highly cited articles. Strong growth in publications is evident in the twelve year period, but the journals in which the researchers publish most frequently differ from the journals in which the most highly cited articles are published. Many of the articles by CDU and JCU affiliated researchers are published in journals outside of the environmental sciences category as defined by Scopus and Web of Science categories and the ERA, however, the research conducted at each university aligns closely with that institution’s research priorities.