In many locations worldwide, groundwater contamination by nitrates is a global problem, resulting from agriculture fertilization and wastewater reuse. Nitrate is considered a harmful compound due to methemoglobinemia, which harms children under the age of 3. The most common approach to remove nitrate is through biological denitrification. In this process denitrifying bacteria can utilize nitrate (and nitrite) as electron acceptors in the oxidation of organic matter. Since the use of oxygen is thermodynamically favourable over nitrate reduction, in treatment processes aimed at denitrification, presence of oxygen should be eliminated. A similar compound present in contaminated groundwater is perchlorate, resulting from ammunition & rocket fuel production. Perchlorate is much more toxic than nitrate and might affect the endocrine system. Removal of perchlorate can be achieved via specialized bacteria, which can use perchlorate as electron acceptor in the oxidation of organic matter. Optimization of nitrate and/or perchlorate removal requires the control of several parameters, including oxygen concentration, pH and C/N ratio. Many studies have reported on the use of alternative carbon sources for denitrification and perchlorate reduction. These sources include dissolved carbon compounds such as methanol and acetic acid, and solid carbon sources such as wood chips and cotton.