Typically when health or environment officials are looking for confirmation of sewage contamination of a water source, they'll go with indicator organisms as evidence. By sampling the water and looking for fecal coliforms, you can tell whether it has been contaminated by bacteria that typically reside in the gut of warm-blooded animals. There's also fluorescein dye if you're looking to confirm that sewage isn't staying in the ground, but that's only effective if the septic failure leads to wastewater being discharged to the ground surface. In other words, if the sewage is making its way into an aquifer, you're not going to see the dye.
There are a couple of problems with fecal coliforms as indicator organisms: they're not necessarily confirmation of human sewage (i.e. just confirmation of some sort of fecal contamination) and they're not overly persistent in the soil. If you're just trying to tell a water system operator that they've got some contamination issues and need to issue a public notification, they work just fine. But if you're looking to confirm that some actual sewage is getting into the water, you're going to have a hard time in front of a judge.
Researchers from Ontario looked at a wastewater plume from a septic field serving a campground that had been in existence for around 20 years (which, incidentally, is about the life span of the average on-site sewerage system), and note that typical indicators of contamination (besides coliforms) are not necessarily unique to sewage, and therefore don't make the best indicators. Chemical compounds that are unique (ibuprofen, pseudoestrogens, carbamazapine) haven't been studied enough to give a clear indication of how long they persist in the environment. They suggest that artificial sweeteners might have value as a wastewater indicator, since they're unique to human waste, resistant to breakdown in normal sewage treatment, and persist in groundwater.
By setting up a number of piezometers and trace gas sampling points along the wastewater plume from the campground, the researchers were able to not only sample the groundwater for the contaminants of interest, but were also able to perform tritium/helium age dating to identify the age of the wastewater plume. Unsurprisingly, their study showed that once you got about 50m away from the sewage dispersal field area, nutrients and pathogens normally found in sewage were reduced to non-detectable levels. Of the sweeteners tested for persistence, they found that cyclamate and sacharrin appeared to degrade quite effectively, while acesulfame and sucralose concentrations remained relatively constant regardless of distance from the septic tank.
Since the acesulfame was detected in levels nearly 1000x higher than background concentrations in the wastewater plume, and degradation didn't occur over approximately 20 years of sewage system use, it presents itself as a potentially viable indicator for wastewater contamination. Apparently, acesulfame is also added to some animal feed, so it could be used as an indicator of groundwater contamination from manure spreading as well.
There's still some further work to be done, since this is just one study of one onsite sewerage system. However, it shows great potential for a new way of determining whether aquifers are being impacted by nearby wastewater. It's worth noting that, from a public health perspective, there is always the issue of cost when speaking to new indicators. The current culture sampling for pathogens is relatively inexpensive, and provides a "good enough" method of identifying contamination. Moving to a compound that requires some analytical chemistry for identification may just be simply too expensive for publicly funded environmental health organizations.
Source: Robertson, W.D., Van Stempvoort, D.R., Solomon, D.K., Homewood, J., Brown, S.J., Spoelstra, J., & Schiff, S.L. (2013). Persistence of artificial sweeteners in a 15-year-old septic system plume. Journal of Hydrology, 477, 43-54.