Although widely studied for their chemical structures and properties (e.g., metal complexation, growth stimulation of planktonic species), humic substances (HS) have been very poorly quantified in fluvial and estuarine waters. In this monthly basis study, we determined HS concentrations (by Adsorptive Square Wave Cathodic Stripping Voltammetry) along the entire river-seawater gradient of the Penzé estuary (NW France), with the aim to characterize the export of these compounds. In this watershed where agricultural activities are predominant, manuring activities were identified as being the main source of dissolved organic carbon (DOC) and HS. HS concentrations varied usually within a narrow range in fluvial waters, i.e., 1.8 ± 0.4 mgC L−1 (150 ± 40 μM), but increased significantly as the first flood of autumn occurred (>4 mgC L−1 in river and upper estuary). At this time, HS accounted for a very high proportion of DOC (>80%). As evidenced by the increasing contribution of HS to DOC, and by the increasing contribution of small colloidal HS species; this autumnal flood increase should be attributed to a greater retention and transformation of organic matter on soils over the hotter, drier, and lighter period preceding the first autumnal flood. In the mixing zone, HS displayed mostly conservative behaviour, although some removals were occasionally observed. Overall, our study suggests that preservation of HS could be relatively important during their transfer across macrotidal temperate estuaries, at least in systems affected by agricultural practices.