Secondary minerals in mine waste materials impose strong controls on water quality by scavenging solutes of concern. This study investigates the mineralogical and compositional characteristics of secondary Fe(oxy)hydroxides and Ca-sulfates, two globally ubiquitous secondary precipitates, in weathered mine waste rock. Bulk analyses show that Si, Ca, Fe, Al, and S-bearing primary phases were the most abundant in the entire samples, but up to a few wt% of secondary Fe(oxy)hydroxides and Ca-sulfates were present as well. In these secondary phases, trace metal impurities like V (37 mg/kg in Ca-sulfates), Cr (23 mg/kg in Fe-oxides and 21 mg/kg in Ca-sulfates), and Cd (up to 15 mg/kg in Fe-oxides and Ca-sulfates) could not be detected by bulk techniques (XRF and XRD), but their deportment to some extent characterized by automated mineralogy, and their spatial distribution assessed at high-resolution through microscale LA-ICP-MS analysis. Element mapping revealed that metal(loid)s were generally enriched at grain rims, reflective of peripheral sequestration through surface adsorption. An exception was V, which was uniformly distributed in the studied secondary Fe-oxides, suggestive of isomorphic substitution during co-precipitation. Factor analysis revealed distinct groups of elements co-associated within each secondary mineral (e.g., divalent transition metal cations versus oxyanionic metalloids), likely caused by similar primary mineral sourcing or a comparable sequestration mechanism. Our results demonstrate the importance of secondary mineral precipitates for scavenging (trace) elements and the insights that can be gained from complementary mineralogical and element analyses for the interpretation of trace element dynamics in waste rock.