Climate warming has accelerated glacier melting, releasing legacy pollutants such as mercury (Hg) into aquatic ecosystems. While the relationship between Hg in glacier meltwater runoff, total suspended particles (TSP), and runoff discharges has been established, the underlying inter-relationships and governing factors remain poorly understood. To address this knowledge gap, we conducted a continuous fixed-point sampling at Laohugou No. 12 Glacier in the northern Tibetan Plateau from June to September 2019 spanning the entire glacier ablation season. Our study analyzed the variations of Hg partition in the meltwater runoff and conducted a comprehensive co-analysis of Hg with TSP and discharge to uncover the dominant factors of Hg input into meltwater runoff. The concentration of total Hg (THg) in the meltwater runoff ranged from 0.7 to 112.6 ng/L, with an average concentration of 26.6 ± 25.1 ng/L. Particulate Hg (PHg) was found to be the predominant partition, while dissolved Hg (DHg) exhibited a notable increase in June and September. THg concentration significantly correlated with TSP concentration (r = 0.94, P < 0.01), exceeding the correlation with discharge (r = 0.76, P < 0.01) during the entire ablation period. However, further examination during varying hydrological periods revealed differing associations among Hg speciation concentrations, TSP concentration, and discharge. During the rising limb of the hydrograph, THg (r = 0.86, P < 0.01) and PHg concentrations (r = 0.87, P < 0.01) exhibited a significant correlation with TSP concentration, primarily driven by TSP, implying that Hg availability determines the Hg input into meltwater runoff. Conversely, during the recession limb of the hydrograph, THg concentration was primarily influenced by discharge (r = 0.85, P < 0.01). PHg (r = 0.84, P < 0.01) and TSP (r = 0.97, P < 0.01) concentrations were strongly influenced by discharge, indicating that hydraulic action is the dominant factor affecting Hg input. Our study elucidated the impact of glacier hydrological processes on Hg transport, revealing the dominant factors of Hg input during different hydrological periods. This contributes to a deeper understanding of Hg input into meltwater runoff and improves predictions of Hg export through glacier melt in high mountain regions.