Bacteria monitoring is a critical part of wastewater management. At tropical wastewater stabilization ponds (WSPs) in north Australia, sanitation is assessed using the standard fecal indicator bacteria (FIB) Escherichia coli and Enterococci. However, these bacteria are poor surrogates for enteric pathogens. A focus on FIB misses the majority of pond-bacteria and how they respond to the tropical environment. Therefore, we aimed to identify the unknown pond bacteria and indicators that can complement E. coli to improve monitoring. Over two years, we measured the bacterial community in 288 wastewater samples during the wet and dry seasons. The WSP community was spatially and temporally dynamic. Standard pond-water physicochemical measures like conductivity poorly explained these community shifts. Cyanobacteria represented >6% of the WSP bacterial population, regardless of sample timing and location. Fecal bacteria were abundant in the first pond. However, in downstream ponds, these bacteria were less abundant, and instead, environmental taxa were common. For each pond, we identified a bacterial fingerprint that included new candidate bacterial indicators of fecal waste and processes like nitrogen removal. Combining the new indicators with standard FIB monitoring represents a locally relevant approach to wastewater monitoring that facilitates new tests for human fecal pollution within tropical climates.