In the last few decades, the presence of pharmaceutical products in the environment is known under the name of emerging contaminants. These substances can enter the aquatic environment via different sources, as parent compounds, metabolites or a combination of both. In this work, we have investigated the presence of four pharmaceutical active compounds belonging to the group of Non-Steroidal Anti-Inflammatory Drugs (NSAIDs), in wastewater, surface water and drinking water of Algiers, which have a direct impact on the Mediterranean Sea. The target analytes (ibuprofen (IBU), naproxen (NAP), ketoprofen (KET), and diclofenac (DIC)), were extracted from the water samples by using Solid Phase Extraction Oasis^® HLB Cartridges; the identification and quantification were realized by Gas Chromatography–Mass Spectrometry (GC–MS). To obtain the best resolution and precision, N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) was used as the derivatization reagent and ibuprofen-d₃ was used as the internal standard. The obtained recoveries were good, ranging from 82% for ketoprofen to 120% for naproxen with relatively small standard deviations (≤20%). The target compounds were detected in wastewater, influent/effluent with concentrations ranging from 155.5 to 6554 ng/L, implicating removal efficiencies of wastewater treatment plants (WWTPs), between 30.3 and 95%. The surface water was also contaminated with pharmaceuticals from 72.9 ng/L for diclofenac to 228.3 ng/L for naproxen. In addition, the occurrence of ibuprofen and ketoprofen in drinking water, at concentrations of 142.1 and 110.9 ng/L, respectively, attracts concerns about possible impacts on human health.