The Nenjiang River Basin, as a crucial distribution area for prehistoric cultural sites in Northeast China, is characterized by its abundant water and fishery resources, making it an ideal region for studying the interaction between prehistoric human activities and hydrological conditions. This study, taking Lake Yuejiapao in the Nenjiang River Basin as an example, quantitatively reconstructs the evolution of hydrological conditions and the changes in fishery resources since the Holocene. By integrating regional prehistoric archaeological records, it deeply explores the impact mechanisms of natural resources on prehistoric human survival strategies and settlement evolution. This paper aims to investigate how prehistoric societies, primarily based on a fishing and hunting economy, responded to hydrological fluctuations by adjusting their human-land relationships. The research results indicate: (1) During the period of 13~7 cal kyr BP (Early to Mid-Neolithic), hydrological conditions and fishery resources continuously increased, with the maximum fish productivity reaching 1928.55 t/year, capable of supporting a population capacity of up to 9180 people, sufficient to meet the protein demands for human survival at that time. Ample and stable water and fishery resources promoted settlement development and the formation of a sedentary mode during this period; (2) Around 5.5 cal kyr BP (Late Neolithic), possibly affected by unstable climate fluctuations and floods, the settlements in this region experienced an overall decline. However, the per capita resources might have relatively increased at this time, leading to relatively comfortable individual living conditions and fuller utilization of fishery resources; (3) After approximately 5.0 cal kyr BP, water resources decreased, and fish productivity dropped to 1198.53 t/year. The minimum population capacity supported by these resources reduced to 5705 people. By the Mid-Bronze Age, the fishery resources in Lake Yuejiapao could no longer fully meet the huge demands brought by the rapidly growing population. To address this, people gradually increased livestock rearing to obtain more stable protein, in order to maintain social development; (4) Hydrological changes also promoted the evolution of settlement spatial patterns. Neolithic settlements were located closer to water bodies, while later settlements migrated to higher grounds, reflecting an active avoidance of flood disasters. This paper, for the first time, quantitatively reconstructs hydrological conditions and changes in fishery resources, revealing the close relationship between hydrological conditions and human survival, settlement location, and subsistence patterns. It provides a new perspective for further research on the interaction between humans and the natural environment.