Transport of carbon, major and trace elements by rivers in permafrost-affected regions is one of the key factors in circumpolar aquatic ecosystem response to climate warming and permafrost thaw. A snap-shot study of major and trace element concentration in the Lena River basin during the peak of spring flood revealed a specific group of solutes according to their spatial pattern across the river main stem and tributaries and allowed the establishment of a link to certain landscape parameters. We demonstrate a systematic decrease of labile major and trace anion, alkali and alkaline-earth metal concentration downstream of the main stem of the Lena River, linked to change in dominant rocks from carbonate to silicate, and a northward decreasing influence of the groundwater. In contrast, dissolved organic carbon (DOC) and a number of low-soluble elements exhibited an increase in concentration from the SW to the NE part of the river. We tentatively link this to an increase in soil organic carbon stock and silicate rocks in the Lena River watershed in this direction. Among all the landscape parameters, the proportion of sporadic permafrost on the watershed strongly influenced concentrations of soluble highly mobile elements (Cl, B, DIC, Li, Na, K, Mg, Ca, Sr, Mo, As and U). Another important factor of element concentration control in the Lena River tributaries was the coverage of the watershed by light (for B, Cl, Na, K, U) and deciduous (for Fe, Ni, Zn, Ge, Rb, Zr, La, Th) needle-leaf forest (pine and larch). Our results also suggest a DOC-enhanced transport of low-soluble trace elements in the NW part of the basin. This part of the basin is dominated by silicate rocks and continuous permafrost, as compared to the carbonate rock-dominated and groundwater-affected SW part of the Lena River basin. Overall, the impact of rock lithology and permafrost on major and trace solutes of the Lena River basin during the peak of spring flood was mostly detected at the scale of the main stem. Such an impact for tributaries was much less pronounced, because of the dominance of surface flow and lower hydrological connectivity with deep groundwater in the latter. Future changes in the river water chemistry linked to climate warming and permafrost thaw at the scale of the whole river basin are likely to stem from changes in the spatial pattern of dominant vegetation as well as the permafrost regime. We argue that comparable studies of large, permafrost-affected rivers during contrasting seasons, including winter baseflow, should allow efficient prediction of future changes in riverine ‘inorganic’ hydrochemistry induced by permafrost thaw.