River pollution can harm human health through direct contact, drinking water, and the consumption of contaminated fish and irrigated agricultural products. Surface water and Nile tilapia (Oreochromis niloticus) samples were collected monthly from July 2022 to June 2023 at three sites (El-Rahawy, Sabal, and Tala) along the Rosetta Nile branch in Egypt to monitor the presence of eight trace elements. The potential human health risks from consuming contaminated fish were also assessed. Iron and manganese were consistently detected in all water samples across most seasons and locations, with concentrations generally below the WHO permissible levels. All 72 analyzed fish muscle samples were found to contain trace elements. The mean concentrations of metals in the fish muscle samples, in descending order, were: iron > zinc > copper > manganese > tin > antimony > lead > mercury. Significant spatial and seasonal variations were observed in both water and fish samples. El-Rahawy was identified as the most contaminated site, with summer exhibiting the highest contamination rate compared to other seasons. Fish samples collected from El-Rahawy demonstrated the highest bioconcentration factor (BCF) values for most elements, particularly mercury, lead, iron, manganese, and antimony. Target hazard quotient (THQ) calculations for the trace elements in Nile tilapia muscles revealed that all trace elements, except antimony, had THQ values below 1, suggesting that consuming Nile tilapia from these sites is unlikely to cause adverse health effects. However, THQ values for antimony exceeded the threshold of 1, indicating a potential health risk for consumers. Although the detected trace elements in the fish were below the permissible toxicity limits, some could pose a future threat to human health, necessitating further studies, ongoing monitoring, and preventive measures.