Groundwater plays an important role in New Zealand water supplies and hence monitoring activities are conducted regularly. Most monitoring programmes aim to evaluate groundwater chemistry and almost completely overlook the microbial component in this ecosystem. In our present study, the bacterial community structure of groundwater in the Wairarapa Valley was examined using the terminal restriction fragment length polymorphism (T-RFLP), and relationships between bacterial community structure and groundwater chemistry, aquifer confinement and groundwater usage were explored. In addition, the results from this study were compared with a previous T-RFLP survey of the same area in an attempt to detect changes in bacterial community structure over time. The data obtained suggested that bacterial community structure was related to groundwater chemistry, especially to redox conditions. Species composition showed minimal variation over time if groundwater chemistry remained unchanged. These findings reflect the potential of using bacterial communities as biological indicators to evaluate the health of groundwater ecosystems. We suggest that it is important to include this type of broad bacterial diversity assessment criteria into regular groundwater monitoring activities.