The Leanyer Sanderson Wastewater Stabilisation Ponds were built in 1972 and are the largest in Northern Australia . Before this study, the knowledge of pond bacteria was limited to the culturable Escherichia coli and enterococci . Unfortunately, a focus on these bacteria misses the majority of resident pond bacteria, their responses to the tropical environment, and the dynamics of important bacteria like nitrogen cyclers. The thesis primary research objectives were to (1) identify the microbial community composition in the ponds; (2) identify the genes and microbes responsible for pond nitrogen cycling; and (3) investigate how the microbial community responds to desludging. To address objectives (1) and (2), 288 wastewater samples were collected at the inlet, middle and outlet of Sanderson Ponds 1, 2 and 5 in the morning (6 am) and afternoon (1 pm) during the early wet and dry seasons. For objective (3), 96 samples were collected in a similar manner from Leanyer Pond 2 before desludging and then one week, six months, and 12-months after . Measurements included both in situ physico-chemistry and microbial DNA (or RNA). The 16S rRNA gene was sequenced to determine the bacterial community composition and the Functional Gene Array used to determine the activity of nitrogen cycling genes. The results showed that bacteria typically associated with the human gut are replaced by environmental bacteria as effluent progresses through the ponds and that desludging improves the removal of faecal bacteria and nitrogen. The study determined where and how nitrogen is removed from the pond system. For each pond, a unique fingerprint was identified and consisted of faecal and environmental bacteria-indicators that can be used for pond management and for developing new tests for human faecal pollution in the environment . Thus, demonstrated that DNA based detection methods can provide powerful and cost-effective monitoring tools that can be used both by wastewater managers and environmental regulators.