Groundwater, a vital freshwater source, faces threats from natural and human-induced factors, particularly seawater salinization in coastal aquifers. This study assesses the impacts of seawater intrusion and heavy metals (HMs) on groundwater quality (11 aquifers and 2 drains) in Egypt's El-Omayed area along the Mediterranean coast. Several parameters were measured including pH, electrical conductivity (EC), total dissolved solids (TDS), major ions, and seven HMs. Seawater intrusion, geochemical mechanisms, and hydrochemical faces of water, were evaluated by ion deviations (), Piper, Gibbs and Chadha plots, and various ionic ratios. The water quality indices (WQI, EWQI, and impWQI), and heavy metal pollution index were employed to assess water suitability for drinking, while EC, total hardness (TH), sodium absorption ratio (SAR), permeability index (PI), etc., were used to evaluate water suitability for irrigation. The results indicated that Na–Cl hydrochemical facies were predominant, suggesting significant salinization, and the ion-exchange mechanisms (dissolution-evaporation) influenced by seawater intrusion regulate the groundwater geochemistry. Seawater fractions (%) ranging from 0.012% to 20.89%, along with the positive mixing ratios () of and in all stations, indicates significant ion addition due to seawater intrusion. Although HM concentrations (Fe > Zn > Ni > Cu > Pb > Mn > Cd) within the WHO permissible levels for drinking, the high EC and TDS values suggest substantial saltwater intrusion. WQI, EWQI, and impWQI ranged from 86.53 to 1203.04, 89.14 to 1091.02, and 93.81 to 813.70, respectively, categorizing ∼60% of stations as “very poor,” 1–15% as “poor,” 15–23% as “moderate,” and 1% as “good”. According to FAO, about 38% of stations exhibit moderate hardness (75 < EC < 150), while 69% are permissible for irrigation (EC < 3000). The majority of samples are unsuitable with SAR>12; however, the PI% suggests suitability with PI > 75. Overall, most groundwater in the El-Omayed area is unsuitable for drinking and irrigation without pre-treatment, highlighting the urgent need for effective management and remediation to mitigate seawater intrusion and enhance water quality.