Estuaries serve as nursery grounds for many marine fish species. However, increasing human activities within estuaries and surrounding areas lead to significant habitat quality degradation for the juveniles. In recent years, plastic pollution has become a global environmental issue as plastic debris are found in all aquatic environments with potential adverse impacts on marine biota. Given the important ecological role of estuaries and implications of microplastics (MP) in ecosystems, here we assess the occurrence, number, size, and polymer types of MP ingested by wild and caged juvenile European flounder (Platichthys flesus). We deployed caged fish for 1 month at five sites in three estuaries in the eastern English Channel. The Seine estuary, heavily impacted by manmade modifications and one of the most contaminated estuaries in Europe, was compared to two smaller estuaries (Canche and Liane) less impacted by industrial activities. We found that juvenile flounders (7–9 cm) were vulnerable to plastic ingestion. Seventy-five percent of caged fish and 58% of wild caught fish had the presence of MP items in their digestive tract. Fibers (69%) dominated in the fish’s digestive tract at all sites. An average of 2.04 ± 1.93 MP items were ingested by feral juvenile flounder and 1.67 ± 1.43 by caged juvenile flounder. For the caged fish, the three sites impacted by wastewater treatment plant (Liane, Le Havre harbor, and Rouen) were those with the highest percentage of individuals that has ingested MP items. Most of the isolated items were fibers and blue in color. Polymers identified by micro Raman spectroscopy were polycaprolactam, polyethylene terephthalate, and polyurethane. Although other environmental factors may have affected caged fish condition and mortality, we found no significant correlation with the number of ingested MP. However, the high occurrence of MP ingested by juvenile fish on nursery grounds raises concerns on their potential negative effects for fish recruitment success and population renewal. Finally, this study describes, for the first time, the feasibility of using caged juvenile fish as an assessing tool of MP contamination in estuarine nursery grounds.