The Ganga-Sai River Interfluve contains several ox-bow lakes in the fertile Central Ganga plains (CGP). A ~2.20-meter deep sedimentary profile obtained near the Chandra Shekhar Azad bird sanctuary (Nawabganj lake-NL) of the CGP was studied to understand the evolution of the ecosystem and climate using pollen/spores, diatoms, testate amoebae, environmental magnetic data,and carbon and nitrogen isotopes. This sedimentary profile is chronologically well-constrained by five radiocarbon (14C) dates. Between 4.6 and 4.4 ka, the sandy sediment and pollen evidence for riparian forest, the absence of aquatic pollen and sponge spicules suggest scant water in the vicinity through the river channel. A semi-closed fluvial ecosystem between 4.4 and 4.2 ka is indicated by testate amoebae, sponge spicules and arboreal pollen. At least two intermittent warm conditions prevailed between 4.6 and 4.2 ka. Between 4.2 and 2.8 ka, high aquatic pollen, diatoms and testate amoebae indicate a lake ecosystem. By ~2.8–0.9 ka the gammoscleres from sponges formed during dry seasons indicate recharging during monsoon as the river shifted. Thereafter, agricultural pollen ( Brassica and Apiaceae) indicates a further shift in the lake boundary exposing land. The highly sandy texture, fluctuating δ13C, δ15N and magnetic mineral values indicate an unstable fluvio-lacustrine deposition inducing hydroecological changes influenced by intermittent about 5–6 humid and dry climatic conditions since ~4.6 ka to present. The calcrete layer in the bottom sediments shows high aridity in CGP between ~5 and 4.6 ka reaching the climax cold-dry event of ~4.2 ka recorded worldwide. The spectral analysis of palynological data from NL and the contemporary Barela Lake, reveals de Vries and Gleissberg cycles of low and high solar irradiance at centennial to multi-centennial scale during the Holocene. The impact on vegetation, sediment depositional dynamics, and shift in river channel was more rapid showing the dominance of ~200 years. periodicity post ~5 ka as compared to ~300 years of dominance prior to this. This centennial timescale is of great speculation for future climate predictions in CGP coupled with the anthropogenic forcings.