Twelve selected pharmaceuticals including antibiotics, analgesics, antiepileptics and lipid regulators were analysed and detected in water samples collected from 18 sampling sections along the three main urban rivers in Yangpu District of Shanghai, China during four sampling campaigns. Besides, algal growth inhibition test was conducted to preliminarily assess the eco-toxicology induced by the target pharmaceuticals in the rivers. Mean levels for most of target compounds were generally below 100 ng/L at sampling sections, with the exception of caffeine and paracetamol presenting considerably high concentration. The detected pharmaceuticals in the urban rivers ranged from <LOQ for propranolol to 8571 ng/L for caffeine. Qiujiang River could be regarded as the most polluted according to total detected pharmaceutical concentrations. The target pharmaceuticals varied and fluctuated irregularly from the upstreams to the downstreams of the three rivers, indicating the wastewater inputs from non-point sources and their individual different characteristics of transference and transportation. Preliminary eco-toxicological risk assessment showed that the presence of azithromycin, clarithromycin and caffeine may present an ecotoxicological risk in the urban rivers. For other tested pharmaceuticals the inhibition effects of single substances in the urban aquatic environment, based on the algae inhibition tests, were very imperceptible.