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Gravel/sand filters have been shown to be highly effective in removing BOD5 from wastewater. The question is what happens to the organic carbon in the filter. Is it trapped or converted to another form of carbon? The purpose of this study was to examine the transformation and accumulation of various carbon fractions of the wastewater in sand filter systems. Twelve columns containing layers of sand and gravel were constructed for the experiments. The twelve columns were divided into six groups allowing for a duplicate of each experimental treatment. Each group received a different loading rate, dosing frequency, pH adjustment, or received supplemental air for seven months. In every case, BOD5 removal from cheese processing wastewater exceeded 99% for all of the variables tested, making gravel/sand bioreactors a viable option for treatment of cheese processing wastewater. Dosing the system twelve times a day rather than only once per day facilitated the conversion of organic to inorganic carbon and resulted in less oxygen demanding carbon trapped in the filter. The application of more frequent, small doses showed a slower progression of filter clogging. Adjustment of pH, while having no impact of BOD5 removal, did have an impact on the accumulation of slowly degradable carbon trapped in the filter. The adjustment to a more neutral pH facilitated the degradation of the slowly degradable organic carbon over the seven months of the experiment. The accumulation of slowly degradable carbon trapped in the filter may lead to premature filter clogging.