Pharmaceutical substances and their residues are increasingly present in the environment. Therefore, attempts at their removal are made by using different processes. Increasingly important among these processes are those modeled on natural phenomena which occur in wetland ecosystems, called technical scale constructed wetlands. Microbial degradation is an important process in these constructed wetlands. The biodegradation of chemicals often involves a complex series of biochemical reactions and usually varies with the microorganisms involved. The objectives of this study were to determine the impact of sulfamethoxazole and diclofenac on ammonia oxidizing bacteria and other parameters of wastewater in the microcosm of down-flow constructed wetlands. The Spearman correlation coefficient attained negative values in the case of comparison of the Shannon biodiversity index and the parameters of purified wastewater. This dependence was pronounced. In the case of pharmaceutical substances dosed with wastewater, the Spearman correlation coefficient assumed positive values. The highest value assumed by the Spearman correlation coefficient (0.9) was for the removal of diclofenac and Shannon index values for the planted columns, with a very high relationship. For unplanted columns, this value equaled 0.6. For sulfamethoxazole, the value for planted columns was 0.7, and for unplanted -0.7. The presence of plants did not have an impact on the Shannon biodiversity index.