Lakes in arid and semi-arid regions have an irreplaceable and important role in the local environment and wildlife habitat protection. Relict Gull (Larus relictus), which is listed as a “vulnerable” bird species in the IUCN Red List, uses only islands in lakes for habitat. The habitat with the largest colonies in Hongjian Lake (HL), which is located in Shaanxi Province in China, has been severely threatened by persistent lake shrinkage, yet the variations in the area of the lake and the islands are poorly understood due to a lack of in situ observations. In this study, using the Modified Normalized Difference Water Index, 336 Landsat remote sensing images from 1988–2015 were used to extract the monthly HL water area and lake island area, and the driving factors were investigated by correlation analysis. The results show that the lake area during 1988–2015 exhibited large fluctuations and an overall downward trend of −0.94 km2/year, and that the lake area ranged from 55.02 km2 in 1997 to 30.90 km2 in 2015. The cumulative anomaly analysis diagnosed the lake variations as two sub-periods with different characteristics and leading driving factors. The average and change trend were 52.88 and 0.21 km2/year during 1988–1998 and 38.85 and −1.04 km2/year during 1999–2015, respectively. During 1988–1998, the relatively high precipitation, low evapotranspiration, and low levels of human activity resulted in a weak increase in the area of HL. However, in 1999–2015, the more severe human activity as well as climate warming resulted in a fast decrease in the area of HL. The variations in lake island area were dependent on the area of HL, which ranged from 0.02 km2 to 0.22 km2. As the lake size declined, the islands successively outcropped in the form of the four island zones, and the two zones located in Northwest and South of HL were the most important habitats for Relict Gull. The formation of these island zones can provide enough space for Relict Gull breeding.