<p>The Lower Yellow River (LYR) is short of water resources. The imbalance and incoordination of water resources (WR), ecological environment (EE) and social economy (SE) have become the key constraints of regional sustainable development. This paper constructed a water resources–ecological environment–social economy (WES) index system in the LYR on the basis of 28 evaluation indicators. The coordination level of the WES system and the cooperative and competitive relationships among the three subsystems were explored through the coupling coordination degree model and the synergy evolution model. The results showed that (1) there was an overall increase in the development level of WR, EE and SE subsystems. The WR exhibited significant fluctuations in different years, while the SE showed unbalanced distributions in different regions. (2) The coordination level of the WES system indicated a continuous growth from reluctant coordination in 2001–2002 to high coordination in 2022–2023. Shandong exhibited a higher coordination level than Henan. (3) The relationship between WR and EE was predominantly in a non-synergistic state, which resulted in limited development growth for both WR and EE. Relatively, the SE was characterized by weakly synergistic or synergistic state with the other subsystems, indicating a great development potential. To improve the uncoordinated development of the WES system, some measures for enhancing WR utilization efficiency, science and education investment and sewage and exhaust control should be taken in the future. The research results offer guidance for promoting the sustainable and coordinated development of WR, EE and SE in the LYR.</p>