The Henares-Jarama-Tajo river system is the largest drainage basin in the Province of Madrid, Spain. This area is characterized by the presence of intensive urban and industrial activities influenced by a continental Mediterranean climate with rainfalls presenting substantial fluctuations along the different seasons. This research aimed to monitor seasonal variations in concentrations of 22 pharmaceutically active compounds (PhACs) in this river system and to establish the potential risk of sublethal effects on aquatic organisms. A total of 10 sampling sites were selected along the river system with samples collected in each of the four seasons during a year-round schedule. Most of the PhACs detected were present in sampling sites downstream in the vicinity of the most populated cities (i.e. Madrid, Guadalajara and Alcalá de Henares). Only two PhACs, fluoxetine and paraxantine, were detected in all sites regardless of the season, and showed median (+/- interquartile range) concentrations of 21.4 (+/-31.2) ng L(-1) and 8.5 (+/-5.3) ng L(-1), respectively. Other PhACs were detected with a frequency >80% and included, caffeine, diphenylhydantoin, hydrochlorotiazide, ibuprofen, ketoprofen, diclofenac, sulfamethoxazole, atenolol, naproxen, carbamazepine and propanolol. Seasonal variations were observed with the highest concentrations in December and the lowest in September. By combining measured environmental concentrations with toxicity data (either publicly available or obtained experimentally in our laboratory), and by calculating an Maximum Risk Index (MaxRI) that each combination of PhACs should have for non exceeding the risk threshold, a high potential for long-term risk (MaxRI<10) was estimated for most of the sampling sites and sampling dates. This research allowed the characterization of the potential risk for each of the PhACs to exert sublethal effects on aquatic organisms using acute screening methods, justifying the need for chronic data in order to refine the risk of these compounds to aquatic organisms.