The source water protection plan (SWPP) frameworks often face limitations in addressing hydrogeological complexity, particularly for investigating groundwater–surface water interaction (GSI). In the present study, an SWPP framework is proposed to improve understanding of hydrogeological conditions and to investigate GSI using multiple approaches, including hydrochemical analyses, hydraulic gradient assessments, and numerical modeling. The proposed framework was demonstrated in a case study in a northern First Nation community in Canada. Using this framework, a water sampling and monitoring program was implemented to assess the quality of the aquifer and the hydrologically connecting river, with monthly measurements of hydrochemical parameters. Groundwater levels were continuously recorded at the monitoring wells using installed data loggers. Lithological information obtained from all monitoring and geotechnical wells was then used to conduct aquifer mapping, and a regional stratigraphic model was developed based on these data. Iron and manganese concentrations in most samples were higher than the recommended limits of the Canadian Drinking Water Guidelines. A positive correlation of hydrochemical data revealed a potential interaction between the aquifer and the river. Hydraulic gradient analysis showed that the river water level was higher than groundwater levels, indicating that the river is a losing stream contributing recharge to the aquifer. These data were then used to develop a numerical model to quantify GSI components. The SWPP framework can support protection strategies to ensure the effective management of drinking water resources.