During the last few years, Lake Manzala, the largest Egyptian coastal lake, has suffered from the excessive discharge of industrial, agricultural, and municipal wastewater. This study aimed to identify the level of PAHs contamination in the sediments of Manzala Lake, investigate possible pollution sources, and address the associated ecological risk of PAHs on benthic communities. Sixteen priority PAHs recommended by the USEPA, including Naph, Ace, Acthy, F1, Phen, Ant, Flu, Pyr, BaA, Chr, BbF, BkF, BaP, DBA, BghiP, and IP, were monitored in this study. Surface sediment samples were collected from 11 sites in the lake. The results of ∑PAHs fluctuated between 15.92 and 12707.64 µg/Kg, while four-cyclic PAHs recorded 58.31% of ∑PAHs. The PAH source distribution was determined using different isomeric ratios (Ant/(Ant+Phen), Flu/Pyr, InP/(InP+BghiP), BaA/ (BaA+Chr) that suggested pyrolysis as the major input source of PAHs. We used different sediment quality guidelines (SQGs), effect range low (ERL) and effect range median (ERM), threshold effect concentration (TEC), and probable effect concentration (PEC) approaches to infer hazard risk caused by PAHs on benthic communities. Generally, ∑PAHs concentrations were lower than the ERM and PEC values at all sites under study. However, some compounds such as F1, Flu, Pyr and DBA exceeded ERL and TEC levels, which detected a moderate possibility of an ecological effect in the middle sector of the lake. Moreover, based on the toxicity indices (mPEC- mERM-q), the middle sector was the most contaminated and thus it is the most probable site to cause a risk for benthic organisms.