The Wadden Sea in north-western Europe is the largest system of connected intertidal sand and mud flats in the world and is included in the UNESCO World Heritage list. Notwithstanding its ecological value, almost all rivers flowing towards the Wadden Sea are heavily modified with inter-tidal barriers, hampering the migration of diadromous fishes. To mitigate the negative effects of such barriers, fish passes were constructed, but their effectiveness is poorly understood. Since most fish passes are only functional during part of the tidal cycle, migration activity should match this operation window to secure effective migration. In this study we focused on the upstream-migrating behaviour of glass eel (the juvenile stage of catadromous eel, Anguilla anguilla) and three-spined stickleback (anadromous Gasterosteus aculeatus) at nine fish passes along the Dutch Wadden Sea coast. We investigated the presence of sticklebacks and glass eel at the downstream side of intertidal barriers in relation to fluctuations in their environment. Fish were collected with 1x1-m lift nets, with a 2-mm mesh size. In 168 sample days between February and May 2014, 4558 samples were taken and a total of 107,349 sticklebacks and 23,082 glass eel were caught. At all locations, glass eel were most abundant in the hour before high tide, while sticklebacks did not show a significant pattern with environmental variables at all locations, but when they did catches were highest at the start of flood tide. This means that the window of opportunity for migration is different for both fish species and that optimisation of the operation window of a fish pass for glass eel could mean a mismatch for stickleback and vice versa. Knowledge of temporal migration dynamics of fish species is therefore essential for the design of effective fish passes.