Groundwater is an important water resource that must be protected from potential contamination due to anthropogenic activities such as industrial production and agriculture. It is necessary to understand the presence, movement, and persistence of contaminants in aquifers to develop adequate protection plans. Fractured bedrock aquifers with thin overburden cover are very sensitive to contamination, and little is known about transport processes from the ground surface to depth in this setting. Thus, this research was undertaken to improve the understanding of anthropogenic impacts on water quality in a natural fractured bedrock aquifer with minimal overburden protection. This was accomplished through a field-based investigation conducted in an agricultural setting near Perth, Ontario, Canada. The temporal and spatial variations of several contaminants and indicators (including nitrate, E. coli and polybrominated diphenyl ethers) were examined. A unique infiltration tracer experiment was also conducted to simulate the transport of solutes from the ground surface to wells. Results showed that nitrate concentrations were consistent on a daily scale, but varied monthly. In contrast to nitrate, greater bacterial (E. coli) variability was observed daily. E. coli was not identified in some locations for several months. The temporal variability of concentrations is an important consideration for those consuming groundwater in this setting, as concentrations may be acceptable one month while unsuitable another month (or even another day for fecal bacteria). Annual groundwater monitoring will likely not capture maximum concentrations and thus may not protect human health. Polybrominated diphenyl ethers (flame retardants), which had not been previously measured in groundwater, were detected in the study aquifer at concentrations greater than observed in surface water bodies. It is evident that additional surveys of PBDE concentrations in groundwater are warranted. The infiltration tracer experiment showed that solute transport from the ground surface through thin soil to wells in fractured bedrock can be extremely rapid (on the order of hours) although very complex. This is an important consideration for private and municipally owned drinking water systems that draw water from shallow bedrock aquifers. The results of this research demonstrate that protecting water at the source is imperative in order to preserve water quality in sensitive fractured bedrock aquifers with minimal overburden cover.