Research questions in environment science can be decomposed into three basic dimensions: space, time and statistics. The combinations of these three dimensions reflect the diverse perspectives of observations across multiple scales. One can classify these scales into four types: individual, local, meso, and global. Following this multi-dimensional and multi-scale framework, this paper conducts a taxonomic analysis that systematically classifies research questions in environmental science. This taxonomic analysis includes papers from a leading environmental science journal. The results show that the majority of research questions are directed at local and global scale analyses. Studies that incorporate many scales of analysis are not necessarily more sophisticated than studies that investigate a single scale. Nonetheless, it's beneficial to explore more possibilities by investigating data at different perspectives. This taxonomy could help generating research questions and providing guidance for building analytic workflow systems to fill the gaps in future scientific endeavors.