This dataset contains information about the background hydrochemistry and nutrient biogeochemistry of water samples collected from networks of interconnected rivers and lakes. Each water sample was analysed for the concentration of multiple fractions of nitrogen and phosphorus, and for the stable oxygen and nitrogen isotope composition of nitrate. Water samples were collected across the period 2017-2018 from multiple river-lake networks in the English Lake District and the Norfolk Broads. This research was supported by the Natural Environment Research Council (Grant NE/N006453/1: Hydroscape – Connectivity x Stressor Interactions)