Lake Balkhash, one of the largest endorheic lakes in Central Asia, has undergone substantial hydrological and ecological alteration over the past five decades. Using a combination of historical records collected before the 1970s and recent field surveys conducted in 2022–2024, we assessed long-term changes in the freshwater gastropod fauna of the lake and examined its relationship to the species assemblage in the surrounding drainage basin. Across all sources, 22 gastropod species were documented within the basin, of which 15 occurred in Lake Balkhash and 18 in the drainage basin, indicating a generally high degree of faunal overlap despite the region’s small size and low landscape heterogeneity. Temporal comparisons revealed marked shifts in species composition and dominance structure. Several native species that were frequently recorded before 1970 were rare or absent in our recent material, while tolerant taxa such as Radix auricularia, Bithynia caerulans, and Valvata piscinalis increased in prevalence or remained consistently frequent. The invasive North American snail Physella acuta was recorded for the first time in both Lake Balkhash and its basin and was among the most common species in recent samples, highlighting rapid community restructuring. These changes are consistent with documented increases in salinity, eutrophication, and habitat modification following major hydrological alteration of the Ili River inflow. Although species richness in the drainage basin was slightly higher than in the lake, nearly all lake species were also present in the basin, suggesting strong biogeographical connectivity and indicating that the basin may serve as a refugium capable of supporting recolonisation under scenarios of ecological decline within the lake. Overall, this study provides the first integrated assessment of gastropod diversity in the Balkhash system and demonstrates substantial long-term shifts in benthic communities, driven by both environmental change and biological invasion.