Environmental pollution has received considerable attention over the last 50 years. Recently, there has been an increasing interest in pollution of the Nile Delta, Egypt, which is one of the longest settled deltaic systems in the world. Pollution in the delta is increasingly recognized as a serious health concern that requires proper management of ecosystems. Therefore, this project aimed to study the distribution and assess the risk associated with selected trace elements (TEs) in different soils (i.e., marine, fluvial, and lacustrine parent materials) in the northern Nile Delta. Mehlich-3 extraction was used to determine the availability of antimony, vanadium, strontium, and molybdenum in agro-ecosystems in this area and their spatial distributions were investigated. Five indices were used to assess ecological risk. Results showed that TEs were higher in the southern part of the study area because it is affected by multiple pollution sources. The available concentrations of TEs were Sr < V < Sb < Mo. The bioavailability of Sr was highest among the studied TEs. The studied indices suggested the study area was moderately polluted by Sr and Sb. Furthermore, the results showed that marine soils had higher TE levels then lacustrine and fluvial soils. The ecological risk assessment indicated that V and Mo were of natural origin, while Sr and Sb were anthropogenically linked. Therefore, the situation calls for planning to reduce pollution sources, especially in the protected north Nile Delta, so these productive soils do not threaten human and ecological health.