Bacteria monitoring is a critical part of wastewater management and pond sanitation is generally assessed using the standard faecal indicator bacteria (FIB) Escherichia coli and enterococci. However, these bacteria are poor surrogates for pathogens, and provide no information about cyanobacteria. A focus on FIB misses the vast majority of resident pond bacteria and how they respond to environmental variables – particularly in tropical environments. Using 16S rRNA tag sequencing, we measured the bacterial community in 288 wastewater samples in a waste stabilisation pond (WSP) located in the northern suburbs of Darwin, northern Australia. Samples were collected during the wet and dry seasons over two years. Whole-community sequencing improved our understanding of the bacteria in the WSP, challenged common assumptions about the abundance of E. coli and cyanobacteria in the ponds, and revealed that wastewater-associated bacteria are spatially and temporarily dynamic even in ‘simple’ systems. Bacterial community changes were poorly explained by the standard physicochemical measurements such as conductivity, highlighting the need to expand monitoring variables. Cyanobacteria represented greater than 6% of the WSP bacterial population regardless of sample timing and location. Faecal bacteria were abundant in the first (maturation) pond. However, in downstream ponds, these bacteria were less abundant, and instead, non-faecal bacterial taxa were common. For each pond, we identified a bacterial fingerprint that comprised both faecal and non-faecal taxa. These include new candidate bacterial indicators that closely track processes like nitrogen removal and human faecal waste. DNA-based detection allowed us to develop a multi-species approach to wastewater monitoring and to identify indicator families and potential surrogates that could be targeted in future to develop WSP-specific indicator probes. Combining the new indicators with standard E. coli and enterococci monitoring represents a locally relevant approach to wastewater monitoring and new tests for human faecal pollution for tropical climates.