This study presents high-resolution multi-proxy analyses of a well-dated sediment core (BR-1, 19.20 m long) retrieved from the Nile Delta, aiming to reconstruct the Holocene evolution of the Burullus lagoon. In particular, we focus on the morphodynamical processes, sediment provenances and related hydro-climatic changes. The Holocene strata of the lagoon coast comprise Early-Holocene marine transgressive facies and the Mid-Late Holocene retrogressive deltaic facies. Although BR-1 shows no river-channel facies, two peaks of magnetic susceptibility (MS) at ca. 8.0–7.0 ka (also associated with a high sedimentation rate of 50 mm/yr) and 3.5–2.0 ka evoke phases of greater morphodynamic influence of palaeo-Nile branches on the lagoon's development. Both dated peat layers (ca. 13 m and 8 m below MSL) and lagoon muds intercalated in BR-1, together with previously-dated peat strata were benchmarked relatively to MSL for the reconstruction of relative Holocene sea level in the study area. Our results show considerable land lowering on the Burullus coast indicated by a sea-level elevation, ca. 4–1 m lower than the one reconstructed along adjacent coastlines where less land subsidence occurred. The lagoon system began to form after ca. 6.0 ka in response to deceleration in sea-level rise and, being a shallower water body, both macrofauna (Cerastoderma glaucum etc.) and ostracods (Cyprideis torosa) of brackish-water nature emerged. In addition, geochemical data from BR-1 provide insights into environmental change in association with basin-wide hydro-climate fluctuations. Concomitant peaks in Fe/Al, Ti/Al and Cr/Al ratios (mafic origin), together with higher Zr/Al and Hf/Al ratios (felsic origin) before ca. 8.0 ka suggest sediment provenances derived from the White and the Blue Nile during the main African Humid Period (AHP). Since then, Ti/Al kept slightly ascending core-upwards with two pulses at 7.8–7.3 ka and 3.5–2.0 ka, which was asynchronous to Zr/Al and Hf/Al. This corroborates more sediments of basaltic origin transported to the delta coast after the main AHP due to southerly shift in the position of the ITCZ. The two periods of Ti/Al pulse are consistent with the MS peaks in BR-1, suggesting that palaeo-Nile branches remained active during 8.0–7.0 ka and 3.0–2.0 ka nearby.