Land use features can have a significant impact on the flux and stoichiometry of nutrients from the watershed to the sea along the freshwater continuum. Traditional agricultural watersheds designated as a Globally Important Agricultural Heritage System (GIAHS) may have unique features on nutrient dynamics. Here, we conducted seasonal, high-resolution spatial surveys for concentrations of dissolved inorganic phosphorus (DIP) and nitrogen (DIN) and stable isotopes of water and nitrate of the GIAHS in Japan (Kunisaki Peninsula). The highest upstream DIN concentrations (mean = 83 μM) were observed in the non-irrigation period in autumn. 17O isotopes of nitrate suggested that microbial nitrification in forest soil was the primary source (> 95%) of total nitrate. Spatial differences in DIP and DIN concentrations among the upstream, midstream, and downstream waters were small, with high DIN/DIP ratios (> 50) were exported from the watershed to coastal seas. Nutrient concentrations exhibited different dynamics during summer when irrigation was taking place with average DIP concentrations increasing from upstream (0.5 μM) to downstream (2.1 μM) waters. A generalized linear model showed that the proportion of paddy fields, cultivated land, residential area as well as forest were the primary drivers of DIP concentrations. DIN concentrations decreased moving downstream likely due to denitrification in the anaerobic irrigation ponds and paddy fields. This study showed that the traditional agricultural landscapes mitigated the excess DIN loading from forested areas while supplying the essential DIP for coastal production, suggesting an important forest-river-sea connection system that manages nutrient inputs to coastal waters.