The Burullus Lagoon, located in the northern Nile Delta in Egypt, faces significant environmental stress due to the continuous discharge of untreated agricultural runoff and the effects of aquaculture in its southern region, both of which contribute to declining water quality and to the degradation of the aquatic ecosystem. This study aimed to evaluate the effectiveness of using benthic foraminifera and ostracods as biomarkers for monitoring the ecological health of the brackish coastal Burullus Lagoon. In 2014, fourteen sediment samples were collected to assess potential toxic elements (PTEs) pollution in the sediments and evaluate the lagoon's environmental quality. Three pollution indices were calculated: contamination factor (CF), geo-accumulation index (Igeo), and enrichment factor (EF). The mean values of CF and Igeo indicated the following order: Cd >> Pb > Co > Ni > Zn > Cu across all sampling stations. Statistical analyses revealed no correlation between the spatial distributions of organic carbon and PTEs. The holoeuryhaline benthic foraminiferal and ostracod species Ammonia tepida (Cushman, 1926) and Cyprideis torosa dominated the benthic populations, showing tolerance to high levels of organic carbon and PTEs pollution. Low species diversity, a scarcity of living individuals, and the presence of deformed specimens may directly reflect the decline in the ecological quality of the Burullus Lagoon environment. This study highlights the deteriorating ecological health of the lagoon and underlines the utility of combined benthic foraminifera and ostracod assemblages as effective bioindicators for monitoring pollution in the brackish coastal ecosystems of the Nile Delta.