Recovery of injected water is one of the most important aspects of an aquifer storage and recovery (ASR) system and is determined by hydrogeologic, operational, and chemical factors. A common series of reactions resulting in deterioration of water quality is the release of arsenic via pyrite oxidation. Previous work suggests system performance can be affected by altering pumping rates while maintaining a constant volume; this is verified in the conservative transport portion of the study. In addition, this study explores the effect of altered pumping rates on arsenic release via pyrite oxidation. A single ASR well in a confined homogeneous aquifer was simulated for a range of hydraulic gradients and storage durations for ten cycles to quantify the effect of pumping rates on system performance for conservative transport using numerical modeling. Reactive transport capabilities were added to a subset of these models to analyze the effects of altering pumping rates on arsenic release via pyrite dissolution. The simulation results showed that performance improved with higher injection and extraction rates for all combinations of hydraulic gradient and storage period considered, although the magnitude of improvement over the baseline scenario was greater for higher hydraulic gradients and longer storage periods. Extraction rates were more influential on system performance than injection rates, with the best and worst performance experienced during the fast and slow extraction scenarios, respectively. Longer storage periods result in more total arsenic released and higher average recovered arsenic concentrations. Injection and extraction rates have their own impact on arsenic release via pyrite dissolution. Injection rates control the spatial extent of dissolved oxygen around the well, with higher rates resulting in a larger extent. Extraction rates affected the amount of arsenic released by controlling the residence time of dissolved oxygen. Higher extraction rates resulted in less residence time of dissolved oxygen and less arsenic released overall. Both higher extraction and injection rates resulted in lower recovered arsenic concentrations; however, regardless of pumping rate, recovered arsenic concentrations were below the EPA’s MCL by the second cycle. Results also highlight the need to manage sorbed arsenic and the injected water plume carefully in aquifers containing arsenic-bearing pyrite lest arsenic migrates beyond the well’s capture zone and affects downgradient users.