The Ner River valley (central Poland) underwent substantial transformation during the Weichselian–Holocene transition as a result of fluvial processes and climate changes, resulting in the establishment of its present shape in the Holocene. A multiproxy study based on organic deposits from a palaeochannel fill (Lutomiersk–Koziówki) shows that after the channel was cut off during the late glacial termination, it became a shallow oxbow, fed by local springs. In the Boreal period, the oxbow lake was also fed by precipitation and became a telmatic environment overgrown by rush and swamp vegetation. Finally, it was covered by overbank deposits. The first flooding phase (9900–9600 cal. BP) was followed by the accumulation of overbank sediments (after 9500 cal. BP) and flooding increased after ca. 9300–9000 cal. BP. Pollen data provide information on the regional vegetation context for local and regional changes. In the Atlantic period, an increase in both summer and winter temperatures is inferred from the pollen data, corresponding to an expansion of thermophilous deciduous forests. While in general, flooding phases of the Early Holocene are poorly recognised in Eastern Europe, the Lutomiersk–Koziówki site may be considered as one of the reference points for this phenomenon in the region.