Analyses of environmental DNA has the potential to become an integrated tool in fish research and management. We performed a pilot study during the spring migration of fishes from the North Sea into the Wadden Sea and present comparative results from daily fyke catches (20 mm mesh) in the Marsdiep tidal inlet on two locations and results from weekly fish eDNA analyses on three locations, all within 2 km distance. Fish catches were highly similar on the two locations. Also, the fish eDNA composition was highly similar on three locations, showing no significant difference when restricted to the 21 fish species that were also caught with the fykes. However, when small sized species were included, eDNA compositions were significantly different among the three locations. Over ten weeks, from late April to early July, presence-absence calls of fishes based on weekly eDNA sampling at high tide and low tide significantly agreed with calls based on seven days of fyke fishing 1 km westwards. Moreover, seasonal patterns in eDNA concentration (12S rRNA gene copies/L) inferred from quantitative PCR and Illumina HiSeq community composition, corresponded to patterns in wet mass for the eight most abundant fish species in the fyke (>6 weeks present) despite changes in water temperature and changes in fish size class over the season. Small sandeel and gobies, which are important prey for large fishes and birds, were typically missed with the fyke but contributed up to 25-40% of the total fish eDNA pool depending on the sample location.