Rising organic charge in northern freshwaters is attributed to increasing levels of dissolved natural organic matter (DNOM) and changes in water chemistry. Organic charge concentration may be determined through charge balance calculations (Org.−) or modelled (OAN−) using the Oliver and Hruška conceptual models, which are based on the density of weak acid functional sites (SD) present in DNOM. The charge density (CD) is governed by SD as well as protonation and complexation reactions on the functional groups. These models use SD as a key parameter to empirically fit the model to Org.−. Utilizing extensive water chemistry datasets, this study shows that spatial and temporal differences in SD and CD are influenced by variations in the humic-to-fulvic ratio of DNOM, organic aluminum (Al) complexation, and the mole fraction of CD to SD, which is governed by acidity. The median SD values obtained for 44 long-term monitored acid-sensitive lakes were 11.1 and 13.9 µEq/mg C for the Oliver and Hruška models, respectively. Over 34 years of monitoring, the CD increased by 70%, likely due to rising pH and declining Al complexation with DNOM. Present-day median SD values for the Oliver and Hruška models in 16 low-order streams are 13.8 and 15.8 µEq/mg C, respectively, and 10.8 and 12.5 µEq/mg C, respectively, in 10 high-order rivers.