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Biodiversity of benthic eukaryotic microorganisms in highly acidic (pH ≤ 3.5) aquatic environments is limited to species that have developed strategies to tolerate elevated concentrations of H + and dissolved metals and low nutrients levels that commonly characterize these environments. To survive adverse conditions, some algae, protozoa, and fungi have developed mechanisms to make their cell membranes impermeable to protons and maintain cytosolic pH at near neutral levels; others have developed a cell boundary mechanism that blocks H + ions from entering the cell. High concentrations of heavy metals are also toxic, adversely impacting growth by disrupting physiological, biochemical, or metabolic processes. Some algae, fungi, and protozoans are able to tolerate high metal concentrations via metal complexation outside the cell, extracellular binding and precipitation of metals, reduced metal uptake, increased metal efflux, and detoxification or compartmentalization of metals within the cell. In acidic environments, benthic eukaryotic microorganisms form biofilm communities in which they are the dominant members numerically and ecologically. Eukaryotedominated benthic communities produce heterogeneous microenvironments that vary spatially and temporally in their physicochemical character. The eukaryotes in these biofilms can be considered ecosystem engineers as they directly or indirectly modulate the availability of resources to other species within the biofilm. These eukaryote-dominated communities may play a significant role in mediating their environment by actively and passively contributing to metal attenuation through various processes of biosorption and via formation of laminated organosedimentary structures, which may be used as analogs for similar structures in the rock record.