This paper describes a novel autonomous groundwater quality monitoring system which samples multiple wells to evaluate temporal changes and identify trends in groundwater chemistry. In this aquifer system, nitrate and specific conductance are increasing in the shallow aquifer, while invariant changes in deep groundwater chemistry likely reflect relatively slow groundwater flow.The stability of the deeper aquifer over the monitoring period was leveraged to develop estimates of measurement system uncertainty, enabling the identification of subtle variability in water chemistry that may have otherwise been missed.