This work aims at evaluating mercury (Hg) occurrence, spatial distribution and speciation in groundwater of the Isonzo/Soča River upper alluvial plain downstream from the Idrija Hg mine (Western Slovenia). Several wells and piezometers were sampled both in static and dynamic mode. Total (THg) and filtered (FHg) concentrations were generally higher in static (THg, 1.87–855 ng L−1; FHg, 0.20–13.61 ng L−1) than in dynamic mode (THg, 0.08–78.77 ng L−1; FHg, 0.28–6.65 ng L−1). The estimated background value accounts for 2–3 ng L−1. On the basis of hydrochemistry and isotopic composition, the main sources of groundwater were established. Hg concentrations in the Slovenian sector, supplied by local rainfall, are comparable to values measured close to the Isonzo River. Possible further Hg local sources have been suggested. Stability field analysis for the aqueous Hg species revealed that in the presence of chloride Hg solubility may be increased by the formation of chlorocomplexes. Mercury that rarely enters reduced surrounding conditions can be bound to sulphur to form polysulphide species depending on the pH of water. Since Hg-contaminated alluvial sediments of the Isonzo River may act as a secondary Hg source in groundwater, a borehole was dug down to the water table. Mercury content and speciation revealed that cinnabar (HgS) is the prevalent form followed by the matrix-bound Hg (Hgbound). Variations of the physico-chemical boundary conditions, as well as the raising/lowering of the water table, may be locally responsible for the slight variability of Hg concentrations in the aquifer. Display omitted •Hg spatial distribution and speciation in the groundwater of the Isonzo River alluvial plain were investigated.•Two sampling methods (static and dynamic) were compared to study Hg mobility.•Hg content in the groundwater was not affected by the enriched alluvial deposits.•Hg speciation showed that Cl− has a key role in the formation of soluble species.•Hg as cinnabar (HgS) was found to be the dominant form in alluvial sediments.