The occurrence of emerging organic contaminants (EOCs) in wastewaters and the inability of the conventional wastewater treatments plants to deal with them have been pointed out several times over the last few years. As a result, remnants of those compounds released into the aquatic environment present a potential risk for public health. Constructed wetlands (CWs) have been proposed as environmentally friendly, low-cost alternative systems with satisfactory results for different types of contaminants. This study aimed to evaluate the efficiency of a CW system, planted with the halophyte Juncus acutus, to eliminate bisphenol A (BPA) and two antibiotics, namely ciprofloxacin (CIP) and sulfamethoxazole (SMX) under different operating conditions. The behavior of Escherichia coli and enterococcal populations in terms of changes in their resistance profile for the selected antibiotics and the abundance of two resistance genes (qnrA and sul1) were also examined. BPA and CIP were significantly removed by the CW, with an overall removal of 76.2% and 93.9% respectively and with the plants playing a vital role. In contrast, SMX was not significantly eliminated. Moreover, fluctuations in the antibiotic resistance profile of bacteria were observed. Treatment processes affected the response of the two selected bacterial indicators, depending on the conditions employed in each case. Furthermore, increased levels of resistance genes were monitored in the system effluent. This study indicates that CWs, as tertiary wastewater treatment systems, may demonstrate high removal rates for some but not all EOCs. This implies that each EOC identified in the feed stream should be tested assiduously by analyzing the final effluents before their reuse or discharge into water bodies.