The physicochemical characteristics of dissolved organic matter (DOM) strongly influence its interactions with inorganic species such as protons and trace elements in natural waters. We collected water samples at Boknis Eck, a time series station in the Baltic Sea with a low exposure to freshwater inputs, to investigate how seasonal fluctuations impact the proton binding properties of the isolated DOM. We used potentiometric titrations to assess the binding properties of solid-phase extracted DOM (SPE–DOM) over a seasonal cycle. We report and critically analyze the first NICA parameters estimates of carboxylic-like and phenolic-like sites for brackish water SPE–DOM. The total amount of functional groups (QmaxH,tot) showed no seasonal fluctuations and an average value of 136 ± 5.2 mmol·mol C–1. The average proton affinity (logKH) and binding site heterogeneity (m) showed a relatively minor variability for samples obtained between April and September, when the water remained stratified. These results contribute to a better understanding of the ion binding characteristics of DOM in natural brackish waters.