In this study we use a novel approach to evaluate the source(s) of nitrate contamination in a complex coastal environment. Given a low hydraulic gradient, tidal influences, and highly permeable sand and gravel aquifers, a conventional investigation was unable to discern whether a farm was the source of nitrate contamination in surrounding domestic wells. Alternatively, other potential sources of nitrate may be related to local septic fields and household fertilizers. As a novel approach, we evaluated the use of bacteria communities as a groundwater tracer. Bacteria community composition is controlled by measurable environmental factors such as water quality and soil conditions. Additionally, bacteria can be carried by water from source areas into major groundwater flow pathways as a biological colloidal particle. Understanding bacteria transport and biogeography coupled with new rapid techniques for characterizing bacteria populations through 16S rRNA sequencing have made bacteria useful as a practical groundwater tracer tool. In this study, groundwater samples were collected from eight domestic wells and two farm wells. Bacterial DNA was extracted from the well-water samples and underwent 16S rRNA sequencing on an Illumina MiSeq Sequencer. The relative abundances of bacteria groups present in each sample were determined and used to evaluate population similarities and differences. Based on a Bray-Curtis Non-metric Multidimensional Scaling analysis, it was found that the bacteria community structure associated with each well could be divided into three distinct groups. The bacteria communities in the farm wells were found to be distinctly different from the domestic wells which suggests that the farm was not the source of nitrate in the domestic wells. The bacteria communities among the eight domestic wells could be further divided into two distinct groups. It is likely that the bacteria community structure associated with the two domestic well groups is related to the proximity of each well to two surface water bodies; in this case, a brackish river and tidal salt marshes. This study demonstrates the use of bacteria communities as a means to evaluate recharge sources to groundwater. The results of this study also provide a foundation for future work involving this novel method of using bacteria as a groundwater tracer.