Subsurface biological processes, such as biofilm development, modify flow and permeability in fractured rocks, greatly impacting energy production or treatment efficiencies. This study aims to understand biological-hydrological interactions at a bench scale during the progression and treatment of souring (microbially mediated sulfide production). Few bench-scale studies investigate the role of a biofilm on the flow and permeability evolution, sulfidogensis, and nitrate treatment efficacy in fractured rocks. Our experiment consisted of three sandstone columns that represent differing fracture characteristics due to the mode of fracture initiation: one column with no fracture (as a control), one column with a sawcut fracture, and a third column with a fracture induced by Brazilian loading (tensile). We seek to understand the effects of the biofilm-permeability feedback on flow and nutrient transport characteristics of fractured rocks; specifically, we (1) demonstrate how fracture geometries impact the development of the biomass-permeability feedback within the rock fractures and (2) observe the souring trajectory and effects of nitrate treatment. Observed permeability trends demonstrated that bioclogging modified the flow properties of fractured columns such that they became hydrologically similar to those of the control column. While fractures were initially the main sites of sulfate reduction, when fractures were clogged, the flow in the fractured columns transitioned from a fracture-dominated flow to a matrix-dominated flow, impacting the delivery of an electron acceptor/donor to the microbial population, reducing sulfate reduction rates. Experimental data also demonstrated two distinct stages in the biofilm-permeability development. During the initial biofilm development stage, the growing microbial population had increased reaction rates but decreased permeability, i.e., a negative correlation between reaction rates and permeability. In the later stage, when the biofilm had clogged the columns, a series of biofilm shedding and regrowth directly led to reopening and clogging of the flow channels, affecting microbial accessibility to limiting nutrients. As such, a positive correlation between reaction rates and permeability was observed in this later stage. Post experimental measurements of surface elevations of the fractured surfaces revealed that surface elevations in the sawcut column were lower and more evenly distributed than the surface elevations in the tensile column where the more unevenly fractured surfaces potentially better supported the microbial establishment.