The aim of the study was defined as a complementary analysis of molecular interactions between zinc (Zn) and fulvic acids (FAs) at a broad pH range (3–7), different metal concentrations (0–50 mg dm−3) and chemical properties of FAs and their impact on the Zn binding mechanism, stability, and efficiency. The results showed that the complexation reaction prevailed at pH 6 and 7, whereas protons exchange dominated interactions at pH 3. Stability constant of the complexes increased along with pH (logK increased from ~3.8 to 4.2). Complexation was preferred by less-humidified structures of lower molecular mass containing more oxygen groups. The number of fluorophores available for Zn(II) increased from pH 3 to 7 by ~44%. Depending on the pH, complexation involved a bidentate chelate, monodentate and bidentate bridging mode. Zn(II) binding was insufficiently modeled by the classic Stern–Volmer equation and well described by the double logarithmic equation (R > 0.94) as well as by a modified Stern–Volmer formula assuming the existence of available and unavailable fluorophore populations (R > 0.98). The fluorescence ratio of different fluorophores was proposed as an indicator of the binding affinity of various structures. A positive relationship was found between the fraction of accessible fluorophores and Zn(II) binding at pH 7 determined based on proton release (R = 0.91–0.97). The obtained results can find application in controlling the mobility and bioavailability of Zn in different conditions.