DNA barcodes have been shown to be an accurate means for identifying a taxonomically diverse range of species. As a result, this has made DNA barcodes an attractive option for providing species identifications for environmental monitoring. We demonstrate the steps involved in using DNA barcodes to develop a rapid and cost-effective species-based biological monitoring program using macroinvertebrates from the Little Stringybark Creek, Melbourne, Victoria, as an example. We highlight the benefits of using this approach over traditional monitoring, which relies on the morphological sorting and often family identification. We also show how high throughput DNA sequencing (HTS) can be used to rapidly generate DNA barcodes from mixed macroinvertebrate samples. We discuss more broadly what is still needed for using DNA barcodes for routine monitoring and the limitations and pitfalls of this method and how they could be overcome.