Regime shifts are likely to have strong impacts on all trophic levels and their interactions. In addition, weather conditions and sea level rise together with tidal currents may change sediment morphology in coastal areas and estuaries. Here, we studied the effects of these drivers of ecosystems on abundance of seven wader species feeding on macrozoobenthos in the German sector of the Wadden Sea. We hypothesized that regime shift caused decreases in wader abundance and that changes in sediment morphology driven by sea level rise and tidal amplitude affected these changes. We analyzed numbers of waders on a short term, 1998–2016, that matched a large-scale geographical study of sediment morphology in the German sector, and at a long term, 1987–2019. Changes in numbers of waders were estimated as slope of coefficients of the trends of wader species numbers in the two periods. The average (se) year of decreases in numbers of waders was initiated for most species and tidal basins in the year 1992 (± 0.4) that followed a regime shift in the Southern North Sea and in the Wadden Sea in 1988–1989. There were no statistical differences between the years when numbers of waders started to decrease between the northern and the southwestern tidal basins of the German sector, indicating that the drives affected both coastal sections simultaneously. Significant relationships were found between slopes of coefficients of wader species and sediment morphology and physical features as sea level rise and tidal amplitude. Relationships were most pronounced for the long term, 1987–2019 compared to the short term, 1998–2016. We conclude that regime shift and changes in sediment morphology driven by sea level rise and sediment change can affect abundance of migratory wader species in large estuaries and shallow coastal waters.