This study investigated the biogeochemistry of uranium (U), and the co-occurring elements nickel (Ni) and arsenic (As), in colloids and sediments from two meromictic mine pit lakes that have considerably different depths and geochemistry. In order to characterize the processes controlling metal speciation and cycling in the pits, the distribution and speciation of the elements in colloidal size fractions were analyzed using micro- and ultrafiltration in combination with transmission electron microscopy. Sediment traps collected fresh sediments over the course of one year below the chemocline of the pit lakes and were subsequently analyzed by scanning electron microscopy (SEM) for morphology and chemical digestions. The most common particles found in the shallower pit consisted of Ca-O and Fe-O colloids, while the particles in the deeper pit were composed of Ca-S-O. Filtration results showed a higher abundance of metals in larger colloidal fractions in aged samples, suggesting that colloids can act as metal accumulators. Sediment traps showed the formation of Fe-O, Fe-S, Al-Si, and Ce-P phases, which were observed to sorb U and Ni. The overall U removal was calculated to be 0.9 g/m2/year in both pits, despite considerably different geochemical conditions between the two, and the maximum removal rates for As (shallow pit) and Ni (deeper pit) were 4.7 g/m2/year and 0.6 g/m2/year, respectively. Bottom sediments were also collected from both pits, and characterized using sequential extractions, SEM, synchrotron-based X-ray absorption spectroscopy and Laue diffraction techniques. These techniques showed that the stability of metals in the sediment follows the order Ni < U < As. Nickel, found in the exchangeable and acid soluble fractions, could be easily mobilized by changes in aqueous ionic strength and pH. Similarly, pH and redox changes in the water may strongly affect U, due to its dominance in the acid soluble and reducible sediment fractions. U(VI) mineral phases confirmed by spectroscopy and Laue diffraction, such as vandendriesscheite and monazite, which were likely associated with the oxidizable sediment fraction, may increase overall U stability. Arsenic was more strongly bound to the sediments and mostly present in the oxidizable and residual (highly recalcitrant) fractions. The collective results demonstrate the importance of colloidal particles for metal sequestration processes and their potential importance on microbial communities in pit lakes, highlighting the need for improved characterization of colloids in environmental studies.