The hypersaline Lake Urmia, located in Iran, has undergone a significant reduction in size and is currently facing the risk of desiccation. The decrease in water levels, coupled with elevated salinity levels, has initiated ecological degradation, leading to a substantial decline in the region’s waterbird population. This study employs breakpoint analysis to determine the year when the drought event affecting the lake commenced. Additionally, canonical correspondence analysis (CCA) is utilised to elucidate the interaction between environmental parameters and the waterbird assemblages in Lake Urmia over the period 1970–2018. Our investigation identifies the year 2000 as the initiation of the water crisis in Lake Urmia, synchronously coinciding with the decline in the waterbird populations. This finding highlights a significant connection between the majority of waterbird species and the axes of CCA, intricately linked with water availability within Lake Urmia. This revelation underscores the pivotal role of fluctuations in water levels in shaping the dynamics of the lake’s waterbird assemblages. Furthermore, our observations emphasise the importance of even minor improvements in hydrological conditions of the lake, resulting in substantial positive impacts on waterbird populations.