The assessment of biological samples is critical for measuring the health of New Zealand aquatic environments. Analysis of these samples commonly requires species identification and enumeration, which usually involves microscopy or microbiological methods. These techniques can be time-consuming, laborious, and are dependent on taxonomic expertise. Recent advances in molecular methods provide promising tools for assessing environmental samples. A range of molecular techniques are now used in New Zealand including: fluorescent in situ hybridisation; automated ribosomal intergenic spacer analysis; quantitative polymerase chain reaction; and, most recently, next-generation sequencing. The organisms (or targets) and environments monitored are equally diverse, ranging from cyanobacteria, rotifers and invasive fish in lakes, to macroinvertebrates, and biofilm communities in rivers, to bacteria, micro-and macro-algae and invertebrates in marine ecosystems. Despite research and validation demonstrating their potential, the application of these tools by monitoring agencies has been limited. Legislative requirements, costs, and a reluctance to change methodologies, are the most likely reasons for this. This review examines molecular tools that have been previously or are currently used for monitoring aquatic environments in New Zealand, and explores how these, and new techniques, may be applied in the future.