It has long been understood that groundwater and surface water interact, and thus cannot be studied separately. Gaining an understanding of the relationship and connectivity between the two is critical for water management in New Zealand. However, interactions between surface and groundwater are naturally complex, varying both spatially and seasonally due to a multitude of different factors. The aim of this study was to characterise the connectivity between the groundwater of the Waimea Plains in Southland, which has highly elevated nitrate concentrations near the small town of Balfour, and the Waimea Stream, which has also been shown to have elevated nitrate concentrations. The chemistry of the Waimea Stream was characterised and analysed for significant differences between summer low flows and winter high flows. This was done by first analysing a suite of hydrochemical data collected by Environment Southland between September 2012 and June 2014, then undertaking a monitoring programme from late summer condition to winter (February to July 2016). As well as dominant chemical signatures for winter high flows and summer low flows, spatial and temporal variation in in-stream nutrient concentrations was established. The stable isotopic composition water (δ2H and δ18O) and DIC (dissolved inorganic carbon) (δ13C) was also analysed. In both Environment Southland’s data and the author’s monitoring data, a distinct shift in-stream chemistry was identified between summer low flows and winter high flows. Winter high flows had elevated SO4, K, B, and Al, concentrations, a Na:Cl ratio similar to that of precipitation and a significantly elevated SO4:Cl ratio relative to marine aerosols. Summer low flows had elevated Na and HCO3 concentrations, a significantly elevated Na:Cl ratio relative to that of precipitation, and a diminished SO4:Cl ratio. Groundwater was shown to exhibit the same chemistry as summer stream water, with a significantly elevated Na:Cl ratio and a low SO4:Cl ratio. Summer flows are therefore interpreted to be dominated by groundwater, and winter flows are interpreted to be dominantly made up of overland flow and lateral flow through the soil zone. From δ2H and δ18O analysis, the Waimea Plains surface and groundwater appears to be principally sourced from local precipitation. There was no evidence found of any contribution to the Waimea Plains aquifer from the nearby Oreti River. Variation in δ2H and δ18O between the headwater and middle reaches of the Waimea Stream suggested that groundwater was contributing significantly to flow in the middle reaches of the Waimea Stream. This was supported by δ13C analysis which also indicated groundwater connectivity to the Waimea Stream for these same reaches. However, there was limited groundwater connectivity in the lower Waimea Stream, where the strong shift in δ13C was consistent with DIC outgassing. This may be the result of confining bedrock layers beneath the lower Waimea Stream limiting groundwater contributions to stream water. In summer, nitrate concentrations in the mid to lower Waimea Stream were significantly higher compared to those in the upper, hill country-fed reaches. Given the findings from hydrochemical and stable isotope analyses, the elevated nitrate over summer in the mid to lower reaches of the Waimea Stream is likely to result from groundwater entering the Waimea Stream in the mid-reaches. Nitrate concentrations are higher throughout the Waimea catchment during winter, although to a slightly lesser extent in the headwaters. Similarly, dissolved reactive phosphorus (DRP) was elevated over winter. As overland flow is a significant contributor to flow during winter, the winter increase of nitrate and DRP is expected to stem from increased farm run off. Future management of nutrient inputs into the Waimea Stream should therefore focus on limiting winter surface runoff inputs of both DRP and nitrate. Groundwater inputs of nitrate will be much more difficult to ameliorate, although the use of on farm nutrient budgets should help limit the vertical loss of nitrate down into the Waimea Plains aquifer. Future research should investigate the chemistry of lateral flow soil water directly to better characterise soil water and overland or farm runoff inputs to the Waimea Stream, and hence nutrient fluxes of nutrients into the Waimea Stream from non-groundwater sources