Lake Edku is one of the essential northern Egyptian coastal lakes in the Nile Delta and is seriously influenced by man-made pollutants. It receives vast amounts of agricultural, domestic, and fishing waste, particularly from the El-Khairy and Barsik drains. The levels of heavy metals (HMs) in Lake Edku sediments were evaluated using laser-induced breakdown spectroscopy (LIBS) and inductively coupled plasma (ICP) spectrochemical analytical techniques. Also, environmental risk assessment and potential adverse effects on benthic organisms were carried out using different indices and Sediment Quality Guidelines (SGQ). The present study showed that the lake sediment is contaminated to various degrees according to the indices used. The eastern sector was found to be the most contaminated area, and the most polluting elements were Cd, Zn, Mn, and Ni. Cd recorded the highest enrichment factor (FF) values (31.1–36) and contamination factor (CF) values (4.8–5.4) at the eastern sites, indicating very high enrichment and significant contamination. In addition, many HMs, particularly Co, Ni, Mn, and Cd, exceeded the threshold effect concentration levels (TECs) and probable effect concentration levels (PECLs), recording potentially harmful effects on sediment-dwelling organisms. For example, the average content of Co (9.62 mg/kg) is much higher than its TECs and PECLs values. It was also found that LIBS's results agreed with the ICP results. These findings demonstrated the potential of using LIBS as a significant quantitative analytical method to assess the HMs in the sediments of water bodies. The study's outcomes will warn decision-makers, encouraging them to adopt more suitable policies and action plans toward sustainable development that reduce environmental risk and preserve the lake's natural ecosystem.