The incorporation of water bodies into city surroundings is gaining popularity as metropolitan areas expand rapidly. Maintaining the ecological health of these lakes poses challenges for ecologists and local government officials, given the influence of human activity on hydrological and hydrochemical properties and the resident organisms. Lake Taldykol serves as an illustrative example of how substantial human involvement disrupts the natural equilibrium of water bodies. This disruption offers a valuable model for studying ecological succession patterns amid fluctuating hydrological conditions. The primary objective of this study was to understand how the decreasing water supply in Astana’s lake system affects the biodiversity of aquatic fauna. Studies on the fauna in the vicinity of Taldykol Lake were conducted from 2020 to 2022. The research classified species and quantitatively evaluated the fauna of the lake and its adjacent coasts. The quantitative data was then utilized to calculate the Shannon index for each unique biome. Results indicated a significant impact on the quantity and distribution of species due to a 65% reduction in the lake’s area. Several species emerged as particularly sensitive environmental indicators. Notably, the Shannon index decreased by 0.8 points (30%) from an initial value of 2.7 to 1.9 as the water area decreased by 2,800,000 square meters (65%), and the water volume decreased by 3,098,000 cubic meters (71%). This reduction highlights the ecological implications of the changing lake conditions on biodiversity and overall water quality.