Nutrient pollution in groundwater is widespread throughout the United States due to excess nutrients from land-use practices recharging to groundwater. As nutrients slowly travel along groundwater flow paths, microbial communities within the aquifer may be limited in their capacity to fully remove excess nutrients. Where groundwater flow paths connect with surface water sediments (i.e. groundwater seeps), the presence of organic carbon and diverse microbial communities may promote biogeochemical processing that reduces nutrient loading to surface waters. We used handheld thermal infrared cameras and the natural temperature contrast between stream and groundwater temperatures in summer to extensively characterize locations of groundwater seeps (n > 300) along 26 km of the Farmington River in central Connecticut. We sampled discharging groundwater from 80 identified groundwater seeps along the continuous 26km study reach for major anions, total carbon and nitrogen, denitrification (N₂), greenhouse gases (CO₂, N₂O, CH₄) and dissolved oxygen to better understand spatial heterogeneity in groundwater seep biogeochemistry and its relationship to surrounding watershed characteristics. We observed extensive spatial heterogeneity in nitrate, di-nitrogen gas, dissolved oxygen, and greenhouse gases. Concentrations of nitrate differed by a factor of .5 at groundwater seeps taken within 10 m of each other. Dissolved oxygen and nitrate concentrations were weakly correlated (R² = .18, p <.005), while di-nitrogen gas and nitrate concentrations were not correlated, indicating nitrate reducing reactions are minimal as groundwater discharges to surface water. Historical land cover data from 1985 to 2015 was combined with a MODPATH groundwater model to link modeled groundwater flow paths and residence times (2-40 years) to land cover at time of recharge. We found no significant correlation in nitrate concentrations and our historical source area land cover analysis suggesting that groundwater mixing and biogeochemical processes within the aquifer may mask any connection to land cover at recharge. Our research highlights the importance of better understanding groundwater nutrient processing along groundwater flow paths throughout river networks.