Although the technology of coal mine underground reservoirs has been widely applied in the Western China, little is known about the variation of water quality induced by the removal transformation of nitrogen and dissolved organic matter (DOM) rich in mine water during its storage and transport in a coal mine underground reservoir. Column experiments were carried out at 30 °C and at Darcy fluxes ranging from 0.32 cm/h to 0.64 cm/h to investigate the transport parameters and dynamic changes of nitrogen and DOM in a simulated underground reservoir filled with coal gangue, which was composed of sandstone and mudstone. Results showed that chloride transport could be described by the convection-dispersion equation (CDE) well at a Darcy flux of 0.32 cm/h, wherein the dispersion role was obvious. Despite the high level of nitrite in the influent, the effluent concentrations of nitrite and nitrate fluctuated around the background values through complete denitrification. And the removal of total nitrogen (TN) with efficiencies between 55.1% and 76% were highly correlated with nitrite denitrification. Ammonification of organic nitrogen got weakened over time and the content of ammonium ion tended to be stable at the level of that in the input mine water. The delayed breakthrough curves of chemical oxygen demand (COD) and dissolved organic carbon (DOC) at a Darcy flux of 0.32 cm/h could be attributed to their adsorption onto the coal gangue during their transport through the simulated underground reservoir. Due to the variations of microbial and compositions of the input mine water, the removal efficiencies of COD and DOC increased slightly from 62% to 68%, 56% to 63%, respectively, when the Darcy flux increased from 0.32 cm/h to 0.62 cm/h. The findings would be helpful in evaluating the effectiveness of post-treatment of mine water during its storage in an underground reservoir in coal mine areas of Western China.