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Globally, habitat loss has been deemed a major threat to wetland bird populations. However, the underlying mechanism of population declines and variations in the birds’ vulnerability throughout their annual cycle is challenging to determine, yet critical for development of targeted conservation strategies. Over seven years, landscape water availability explained occupancy of breeding territories best when breeding performance, migratory performance, and annual survival of the White-naped Crane (Grus vipio) population in eastern Mongolia were studied. Also, the hatching success of eggs was positively correlated with water availability in addition to plant productivity. High ambient temperatures and large numbers of herder families (and hence more livestock) negatively affected hatching success. High water availability at Luan, a major stopover site increased migration speed during the cranes’ northbound migration to their breeding grounds. In contrast, when water conditions were favorable, the birds stayed longer at the stopover site during southbound migration. Increased human density reduced the use of the stopover site during northbound migration. Finally, cranes arrived early at the breeding grounds when ambient temperature was high in northeast Mongolia. Combining these findings with historical trends in key environmental factors on their breeding grounds explains the general decline observed in this population of cranes in recent decades. Extrapolating our findings with future climate predictions, the outlook seems poor unless urgent action is taken. Knowledge of the mechanisms underlying White-naped Crane population decline in eastern Mongolia identified in this paper should improve the effectiveness of these actions.