Lake Baikal is the largest freshwater body on Earth, once famous for its pristine conditions. However, the lake and its drainage basin with their unique ecosystems have in recent decades been subject to both climate warming above the world average and severe anthropogenic pressures from mining and agriculture. Although previous studies have targeted various hydroclimatic, geochemical, and biological conditions of the Lake Baikal basin, the heterogeneous nature and large size of the basin leave considerable knowledge gaps regarding ongoing metal contamination of the basin’s suspended sediments and waters. To address these knowledge gaps, the main objectives of this study are to (i) determine regional background values for water and suspended sediment quality with respect to multiple metals (representing undisturbed conditions) and (ii) further evaluate spatio-temporal concentration patterns of these metals, including regions with heavy anthropogenic impacts. We synthesize data from extensive field measurements within the Selenga River basin performed between 2011 and 2016, covering over 100 sampling locations. Results show that although the background metal concentrations (of both dissolved and suspended metal forms) in the alkaline Selenga River waters were close to the world averages, metal concentrations of up to two orders of magnitude above the background values were seen for Zn, As, Cd, Cu, Mo, and Pb in regions subject to anthropogenic impacts (cities and the mining industry). Specifically, dissolved As levels within the Selenga River basin were 2–5 times higher than the world average and well above the global guideline value in several regions. Notable hotspots for anthropogenic impacts of Cd were particularly found in Zakamensk and Ulaanbaatar. Our results highlight clear anthropogenic impacts and large-scale spreading of several pollutants of concern, with risks even to downstream parts including the Selenga delta and Lake Baikal. We expect that these results will aid in increasing the understanding of large-scale metal transport processes, as well as for designing relevant measures to mitigate further spreading of metals to Lake Baikal.