Nitrifying biofilms were grown on 3D-printed nylon with three different surface characteristics (flat, millimeter-scale indentations, and indentations with activated carbon (AC) coating) and were subjected to sequentially increasing aeration-based shear to determine the interplay between surface, performance, and microbial populations towards improved design of wastewater treatment media. Biofilms were evaluated for nitrification, biomass detachment, and microbial composition based on Illumina 16s rRNA sequencing. Indentations provided greater stability over flat with respect to population diversity after detachment events but did not improve ammonia removal. AC-surface biofilm had significantly higher removal than uncoated surfaces at low aeration (1.0 L/min, fine) and significantly lower at high aeration (5.0 L/min, coarse). Principal component analyses of microbial communities illustrated temporal shifts over two similar cycles of growth and shear-induced biomass loss, demonstrating that biofilms grew similar consortia across all surfaces, but tended to revert to earlier individual compositions after shear events.