Most studies on glass eel (Anguilla anguilla) migration are performed in natural estuaries, where they enter freshwater systems to live there for a period of years before they swim back again to the sea to reproduce. In these natural systems, river flows play a major role in attracting and directing migrating eels. However, coastal areas get urbanized more and more and characterized by anthropogenic barriers and hampered or artificial water flows. The effects of these flows on glass eel migration are poorly understood. Therefore, in this study glass eel were sampled at water pumping stations in a constructed part of the Rhine delta in the Netherlands. A mixed linear-effect model was used to determine effects of freshwater flows from water pumping stations on glass eel catch. We found that freshwater flows from water pumping stations had a significant but small effect on glass eel catch. Pumping activity had no significant effect on glass eel catch at sample locations with a continuous freshwater flow from fish passages. However, a low predictive value of the model and low numbers of individuals per sample prohibited strong conclusions on effects of anthropogenic freshwater flows on glass eel migration. More individual tracking techniques should be used to improve understanding migratory behavior of glass eel.