Understanding the total water flows and pollutant loads to the Baltic Sea is important for effective coastal-marine ecosystem management. Current assessments often overlook the unmonitored flows and submarine groundwater discharge (SGD). This study proposes and outlines a conceptual modelling framework for overcoming this common neglect by integrated quantification of (1) the monitored surface water flows, and the unmonitored (2) surface water flows and (3) SGD from land to the Baltic Sea. The study outlines how unmonitored runoff and SGD can be estimated by various quantification approaches based on commonly available hydro-climatic, hydrogeological, and other characteristic catchment data. It also describes how modules for the different monitored and unmonitored discharge components are linked and should be integrated in modelling to total annual, seasonal, or finer-resolved water flows to the Baltic Sea, and analogously also in other coastal regions around the world. Though quantitative modelling remains ongoing, the conceptualization opens pathways to improve assessments and management of freshwater flows and associated pollutant loads to the Baltic Sea.