To better assess the relationship between excess nutrient runoff and plant species diversity in the Egyptian northern coastal lakes, the relationships between aboveground biomass, species diversity, and both micro and macronutrient concentrations in sediment, water, and plant materials were investigated. A total of 38 sampling sites were established for the five Egyptian northern lakes (8 for Bardawil, 10 for Manzala, 8 for Burullus, and 6 for each of Edku and Mariut). Sediment, water, and plant materials were collected and analyzed for both micro and macronutrients including nitrogen (N), phosphorus (P), sulfur (S), magnesium (Mg), calcium (Ca), potassium (K), iron (Fe), boron (B), sodium (Na), and aluminum (Al). Based on the Sørensen similarity index, Burullus and Mariut lakes were very similar (0.70) in their vegetation composition, while Bardawil Lake had no similarity with the rest of the lakes. In sediment, Mariut Lake had the highest total P concentrations (1.3 g kg−1), while Bardawil Lake had the lowest (0.3 g kg−1). Bardawil, a hypersaline lake, had the highest concentrations for both Na and B (9.6 and 0.1 g kg−1, respectively). Among the deltaic lakes, Mariut Lake water bodies had the lowest plant species richness. The current study indicated that the excessive agricultural and industrial nutrient runoff had a greater impact on the nutrient distribution pattern and negatively impacted plant species diversity at the Egyptian coastal lakes. An integrated management plan, including establishing more pretreatment facilities for runoff and wastewater, should be implemented to reduce the nutrient loads from the main industrial and agricultural runoff sources. Moreover, periodic monitoring and assessment for nutrient runoff reaching the lakes are necessary to help reduce eutrophication levels.