We used Great Lakes hydrologic data and bird monitoring data from the Great Lakes Marsh Monitoring Program from 1995–2002 to: 1) evaluate trends and patterns of annual change in May–July water levels for Lakes Ontario, Erie, and Huron-Michigan, 2) report on trends of relative abundance for birds breeding in Great Lakes coastal marshes, and 3) correlate basin-wide and lake-specific annual indices of bird abundance with Great Lakes water levels. From 1995–2002, average May, June, and July water levels in all lake basins showed some annual variation, but Lakes Erie and Huron-Michigan had identical annual fluctuation patterns and general water level declines. No trend was observed in Lake Ontario water levels over this period. Abundance for five of seven marsh birds in Lake Ontario wetlands showed no temporal trends, whereas abundance of black tern (Chlidonias niger) declined and that of swamp sparrow (Melospiza georgiana) increased from 1995–2002. In contrast, abundances of American coot (Fulica americana), black tern, common moorhen (Gallinula chloropus), least bittern (Ixobrychus exilis), marsh wren (Cistorthorus palustris), pied-billed grebe (Podilymbus podiceps), sora (Porzana carolina), swamp sparrow, and Virginia rail (Rallus limicola) declined within marshes at Lakes Erie and Huron/Michigan from 1995–2002. Annual abundances of several birds we examined showed positive correlations with annual lake level changes in non-regulated Lakes Erie and Huron/Michigan, whereas most birds we examined in Lake Ontario coastal wetlands were not correlated with suppressed water level changes of this lake. Overall, our results suggest that long-term changes and annual water level fluctuations are important abiotic factors affecting abundance of some marsh-dependent birds in Great Lakes coastal marshes. For this reason, wetland bird population monitoring initiatives should consider using methods in sampling protocols, or during data analyses, to account for temporal and spatial components of hydrologic variability that affect wetlands and their avifauna.