In the light of the European wide efforts to increase the spawning biomass of the European eel, a reliable measurement of the escapement of mature silver eel is necessary to prove the effectiveness of the conservation management measures. The seaward migration of mature eel is commonly viewed as a seasonal phenomenon with concentrated migration peaks occurring in spring and autumn. To verify the assumed seasonal silver eel migration events for regulated lowland rivers, a stow-net system was installed in the Warnow River located in north-eastern Germany. Between 2008 and 2011, the stow-net system was operated from March to December each year. The eel harvest was documented on a weekly base including the documentation of weight and length, the silvering stage and the tissue sampling for the molecular identification of the eel species. During the 4 year monitoring period, a continuous downstream migration of female and male silver eels was observed. Additionally, single migration peaks were recorded in each year occurring between April and December. Moreover, female and male silver eels showed varying downstream migration dynamics. Based on a Chi-squared Automatic Interaction Detection (CHAID) tree analysis, it was shown that during periods of a daily minimum air temperature over 10.4 °C, increased discharge levels and increased wind speeds, higher weekly migration rates of silver eels were likely. Furthermore, the results indicated that both sexes differed in their responses to migration triggering environmental factors. The presented results might be helpful to design more efficient eel conservation management strategies in regulated lowland rivers.