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The liver fluke disease caused by <i>Clonorchis sinensis</i> is one of the most serious food-borne parasitic diseases in China. Many freshwater fish and shrimps can be infected with <i>C. sinensis</i> metacercariae as the second intermediate hosts in endemic regions. Owing to the lack of infected humans and the good administration of pet dogs and cats in cities of non-endemic regions, few fish are expected to be infected with <i>C. sinensis</i> metacercariae in urban lakes. To determine the infection of <i>C. sinensis</i> metacercariae in freshwater fish and shrimps in urban lakes, a total of 18 fish species and one shrimp species were investigated in the East Lake of Wuhan City. Metacercariae were isolated by artificial digestive juice and identified using morphology and rDNA-ITS2 sequences. Five species of fish, <i>Pseudorasbora parva</i>, <i>Ctenogobius giurinus</i>, <i>Squalidus argentatus</i>, <i>Hemiculter leuciclus</i>, and <i>Rhodeus</i> spp., were infected with <i>C. sinensis</i> metacercariae. The overall prevalence of <i>C. sinensis</i> was 32.5%. The highest prevalence was found in <i>P. parva</i> with 57.9%, while <i>S. argentatus</i> exhibited the highest mean abundance (13.9). Apart from the <i>C. sinensis</i> metacercariae, four species of other trematode metacercariae were also identified across twelve fish species in total. Owing to the consumption of undercooked fish and feeding cats with small fish caught by anglers, there is a potential risk that the small fish infected with <i>C. sinensis</i> metacercariae may act as an infection source to spread liver fluke. Given the complete life cycle of <i>C. sinensis</i>, stray cats and rats were inferred to act as the important final hosts of <i>C. sinensis</i> in urban lakes in non-endemic areas.