Microplastics (MPs) are emerging pollutants that pose a significant threat to human health and the environment. Sediments are the main sink for MPs, but there is still much to learn about the factors affecting the distribution of MPs in the sediment. This study aims to investigate the effect of flooding on the spatial distribution of MPs in Wadi Al-Khoud and examine the impact of physiochemical features and human activities on the distribution and abundance of MPs. Sediment samples were collected from 11 sites along the Wadi, including the upstream, midstream, and downstream of the Wadi. The sites were also categorized into five distinctive areas with one or more human activities/land uses. The collected samples were dried and sieved using a 2 mm sieve. Oxidation treatment was applied to remove the organic content using Fenton’s reagent, followed by density separation using a saturated sodium chloride solution. A Stereomicroscope was used for the physical identification of MPs properties and counting, while micro-Fourier Transform Infrared Spectroscopy (µ-FTIR) was used for chemical identification. Risk assessment was performed using the pollution load index (PLI) and polymer risk index (PRI) based on identified MPs' concentration and chemical toxicity. Overall, the average concentration of MPs increased from 194.4 ± 53.3 -2083.3± 218.5 particles/ kg before the rain to 233.3± 27.2 -13166.7± 365.1 particles/kg after the rain, suggesting that MPs in the surrounding watershed washed into the Wadi stream. Flooding also affected the types of MPs, affecting the relative abundance of different shapes, sizes, and colors found in the samples. In both seasons, most common shape was fragments, followed by fibers, while most MPs were between 10-50 µm. The dominant colors were blue, black, red, yellow, green, and white, while PP and PE were the main polymers, with PA, PVC, and CA being found in lower densities. Based on the proximity to the human activities and land use, the MPs abundance was the following: dam > agricultural residential area/residential recreational area > coastal residential area > natural area. The study found significant negative and positive associations between MPs abundance with sand and clay, silt, and TOC, respectively. The PRI and PLI indicate moderate to high MPs pollution levels, with flooding increasing the risk. This study demonstrates the occurrence of MPs in the arid region of freshwater sediment and the effect of climatic factors, sediment properties, and human activities on their spatial distribution.