The Mn/Zn-containing black sediments were formed at the closed N-mine site and used as a common inoculant to set up two different laboratory-scale passive bioprocesses (named Tank-I and Tank-II) to treat mine waters containing 70 mg/L Mn²⁺ and < 1.8 mg/L Zn²⁺. Using CO₃²⁻-free synthetic mine water, Tank-I (a natural zeolite down-flow tank with surface aeration) achieved >97% Mn²⁺ and > 80% Zn²⁺ removal at an hydraulic retention time (HRT) of 15–17 h, while Tank-II (an up-flow tank filled with semi-calcined dolomite with a bottom aeration) removed >87% Mn and > 79% Zn at an HRT of 24 h. Further shortening of the HRT resulted in a rapid decline in performance (Zn²⁺ desorption followed by Mn²⁺ elution) in both tanks. As the semi-calcined dolomite in Tank-II had been passivated and deactivated during the pre-run period, periodic CaCO₃ addition (plus HRT readjustment) was required in both tanks to reverse this performance degradation. Treatment of the real mine water was generally faster and more complete, presumably due to the continuous influx of naturally occurring CO₃²⁻ into the system. This allowed for >99% Mn/Zn removal at HRT 8–15 h in Tank-I and at HRT 17 h in Tank-II. In Tank-I, birnessite was formed as a result of the oxidative removal of Mn²⁺ where the Mn average oxidation state (AOS) progressed from 3.53 to 3.85 through the activity of potential Mn-oxidizing genera such as Bacillus, Pseudonocardia, Brevibacillus, Nitrospira, Methylobacterium, Bosea, Leptothrix, Mycobacterium, Rhizobium and Pseudomonas. While in Tank-II, in addition to abiotic Mn removal by semi-calcined dolomite in the early stages, microbial Mn oxidation activity developed over time to produce woodruffite and birnessite, with Mn AOS progressing from 3.53 to 3.79 through the activity of potential Mn-oxidizing genera such as Methylobacterium and Leptothrix. The microbial community developed very differently between the two tanks, due to the different tank designs. Off-site Pseudomonas SK3 cells co-inoculated only in Tank-I were eliminated by the indigenous community, presumably due to the lack of Zn²⁺ tolerance. Both tanks were effective in treating the target mine water to meet the effluent standard while producing equally stable Mn oxides. Although the two tanks cannot be directly compared in detail due to their completely different designs, the simpler Tank-I design was superior overall in terms of speed and microbial activity and diversity.