The presence of emerging pharmaceutical pollutants in the aquatic environment is generally related to anthropogenic activities such as domestic, industrial and hospital wastewater discharges and landfills. Special attention should be paid to the contamination of surface waters, as they are partly used for drinking water supply, since they directly collect partly untreated wastewater from wastewater treatment plant. Within this paper, the identification, quantification and distribution of pharmaceutical micropollutants, from different complex environmental matrices, respectively: surface water, sediment and biota in the river basins of Arges-Vedea, Buzau-Ialomita and Dobrogea-Litoral and of the Danube River, were achieved. Also, preliminary investigations were carried out regarding the contamination of lakes with active pharmaceutical ingredients (APIs) the metropolitan area of the municipality of Bucharest. Among the pharmaceutical micropollutants identified in the Arges-Vedea river basin, the most frequently detected was paracetamol with a frequency of 69% and antibiotics with a frequency of 65.52%, in the Dobrogea-Litoral basin paracetamol was detected with a frequency of 74.2% and antibiotics with a frequency of 54.84%, while antibiotics were identified in all surface water samples and paracetamol with a frequency of 80% in the Buzau-Ialomita river basin. Considering the contamination of sediments with pharmaceutical residues, these were identified in all studied areas and in biota samples (fish) up to 18.21 ng/g were detected. The preliminary identification of active pharmaceutical ingredients (APIs) from Lakes Plumbuita, Carol, Morii, Alexandru Ioan Cuza (IOR), Herastrau and Tei indicated the frequent presence of several items, such as paracetamol, tinidazole, carbamazepine, moxifloxacin, clarithromycin, and caffeine.