A lush vegetation develops around the numerous wadi estuaries interrupting the Dhofari coast in Southern Oman. Many estuaries still house mangroves of Avicennia marina (Forssk.) Vierh., a very fragile ecosystem that is currently under threat in this area. A rather rich flora, strongly affected by the influence of the monsoon, grows in other estuaries. This study concerns the flora and vegetation of these peculiar habitats with special focus on the plants growing on the different substrates. To gain insights into the pollen diffusion and representation of these plants in the current pollen rain, we analyzed surface soil samples. By evaluating their pollen amounts, we related the modern pollen rain to the abundance/coverage of the plant species typical of the different environments. Rather than a punctual indication of the plants growing at a short distance, our pollen records offer a general picture of the flora and vegetation of the area. This information is crucial for the correct interpretation of pollen records from ancient soils, and underlines the utility of pollen analysis for the reconstruction of the vegetation history.