Current studies explore the viability, applicability and comparison of Pseudomonas aeruginosa and Pseudomonas stutzeri based biological denitrification of waters containing high concentration of nitrate and nitrite waste originating from various agricultural and industrial sources. This process converts the readily soluble nitrates to harmless nitrogen gas through a formation of series of intermediates. Experimental work involved use of varying concentration of nitrates and nitrites with different packing conditions, substrates and were analyzed by UV-Vis spectrophotometer. The parameters such as C/N ratio, temperature and pH were optimized for decreasing concentration of nitrates and nitrites. Best packing materials for nitrate reduction proved to be the agro waste based materials which have potential to be used for nitrate reduction of various waste water samples obtained around the city. Average nitrate reduction rates obtained for agro based waste packing condition exhibited about 96.55% and 95% for Pseudomonas aeruginosa and Pseudomonas stutzeri respectively. When applied for denitrification of waste water sample using the obtained reaction parameters, average nitrate reduction obtained was 53.84% and 33.72% for Pseudomonas aeruginosa and Pseudomonas stutzeri respectively. Based on the obtained observations and experimental results, general bioreactor for denitrification process has been designed.