Burullus lagoon is part of Egypt’s protected area network. The lagoon serves as a reservoir for drainage water discharged from agricultural areas, and the lake’s sediments provide a unique opportunity to record environmental behavior and reconstruct of the heavy metal contamination history. In the present study, the sediment chronology, sedimentation rates, and metal accumulation fluxes were estimated in four sediment cores using 210Pb dating models to evaluate how human activities have affected the coastal environment. Using the radioisotopes 210Pb and 137Cs, radiometric dating was carried out using gamma-ray spectrometry. At the Egypt Second Research Reactor (ETRR-2), the element concentrations were determined using the instrumented neutron activation analysis (INAA- k0 method). Our findings show that the constant rate of supply (CRS), which has been verified with the peak of artificial radionuclide 137Cs, is the best model performed for the chronology of Burullus Lagoon. The average sedimentation rate, according to 210Pb dating models, is 0.85 cm/year. The large variation in sedimentation rates, especially after the 1990s, is consistent with an increase in the anthropogenic flux of heavy metals. This may be led into a significant environmental problem such as reducing the size of the lake and degrading the quality the water in Burullus Lagoon. Enrichment factor (EF) of the studied elements displayed the following order: Cl > Ca > Na > Br > Zn > Ta > Ti > V > Cr > Sc > Mg > Mn > Fe > Hf which is higher than unity. Furthermore, the Nemerow pollution index (PI Nemerow) revealed that pollution was increasing in the direction of the drains and slightly polluted. Consequently, pollutant indices showed that urbanization and industrial development may have increased the depositional fluxes of the metals in sediments over time.