We present an assessment of the dynamics in the influent concentration of hormones (estrone, estriol) and antibiotics (trimethoprim, sulfamethoxazole, tetracycline, ciprofloxacin) in the liquid phase including the efficiency of biological municipal wastewater treatment. The concentration of estradiol, 17-alpha-ethinylestradiol, doxycycline, oxytetracycline, demeclocycline, chlortetracycline, cefuroxime, cyclophosphamide, and ifosfamide were below the limit of detection in all of the sewage samples collected within this study. Two different types of diurnal variation pattern were identified in the influent mass loads of selected antibiotics and hormones that effectively correlate with daily drug administration patterns and with the expected maximum human hormone release, respectively. The occurrence of natural hormones and antimicrobials, administered every 12 hours, shows a daily trend of decreasing contaminant mass load, having the maximum values in the morning hours. The occurrence of antibiotics, typically administered every 8 hours, indicates a daily peak value in samples collected under the highest hydraulic loading. The efficiency of biological removal of both hormones and antibiotics is shown to be limited. Compared to the values obtained in the influent samples, increased concentrations are observed in the biologically treated effluent for trimethoprim, sulfamethoxazole and ciprofloxacin, mainly as a result of deconjugation processes. Ciprofloxacin is shown as the predominant antimicrobial compound in the effluent, and it is present at quantities approximately 10 fold greater than the total mass of the other of the compounds due to poor removal efficiency and alternating solid-liquid partitioning behaviour. Our results suggest that, to increase the micro-pollutant removal and the chemical dosing efficiency in enhanced tertiary treatment, significant benefits can be derived from the optimisation of reactor design and the development of control schemes that accounts for diurnal secondary effluent micro-pollutant and hydraulic loading patterns.