The brine that has been produced from water-dissolved natural gas reservoirs should be returned into reservoirs after the resources have been extracted to prevent the subsidence. However, the re-injectivity of the brine declines gradually; therefore, re-injection wells should be maintained by backwashing treatments. Colloidal materials like biofilms can be observed in solid materials that have been produced by the backwashing from the re-injection wells. Because the brine contains not only dissolved natural gas but also high levels of iodine, the iodine is also extracted from the brine chemically using sulfuric acid and oxidizing agent; therefore, re-injected brine contains sulfate and dissolved oxygen abundantly. These chemicals may stimulate the metabolites of microorganisms that have influences on the clogging; therefore, we considered the influences of these materials on microorganisms that may cause the clogging in this study. Column experiments were carried out using sand and brine that were collected in the gas field. The columns that the brine including indigenous microorganisms, dissolved oxygen and sulfate was injected into were clogged significantly. Iodide-oxidizing bacteria, iron-oxidizing bacteria and sulfate-reducing bacteria were found specifically in clogged columns, suggesting these microorganisms had influences on the clogging. In particular, Iodide-oxidizing bacteria were also found in original brine; therefore, it was assumed to have an important influence on the clogging. Iodide-oxidizing bacteria convert iodide into iodine that corrodes iron in the sand under the presence of dissolved oxygen. Iron (II) ion that has been eluted from the sand is oxidized to iron (III) ion by iron-oxidizing bacteria under the presence of dissolved oxygen. Iron (III) ion forms ferric hydroxide colloid in the brine and it causes the clogging of the porous media. From these mechanisms of the clogging, we can suggest removing dissolved oxygen as the most feasible countermeasures for the clogging.