Residue management is one of the optimistic options for sustaining agroecosystems. In order to investigate NO3 and NH4 dynamism with the application of soybean and cotton residues incorporated with a silty-clay-loam soil (0-30 cm), an aerobic incubation experiment was carried out using three residue treatments (including cotton residue, soybean residue and cotton residue+urea to eliminate immobilization). The residue amount was determined in order to provide 150 Kg ha-1 of Kjeldahl nitrogen after incorporation with soil (this was done using the nitrogen factor method).The samples were incubated for 175 days under a controlled environment at 25 ̊C. The NO3 and NH4 concentration and bacteria, fungi and Actinomycete populations were measured 7, 14, 28, 67, 109 and 175 days after incubation began. The results confirmed microbial activity dynamism during time. Cotton residues revealed a non significant prevalence on soybean residue with respect to cumulative nitrate and ammonia, which were released during the incubation period. In all cases, the cotton + urea treatment was better than both other treatments. These results were not interpretable based on the C:N ratio and the results showed that the lignin content is probably more important than the C:N ratio (lignin percentage of cotton and soybean residues are equal to 0.7-1.6% and 14%, respectively). In this study, the relationship between nitrate and ammonia dynamism with microbial communities have been analyzed.