Although freshwater habitats play a crucial role in most ecosystems in the world, little is known on their functioning in tropical regions even in regard to the most often studied avian communities. In this study, counts on waterbirds were conducted in dry and wet season (in years 2001–2008) in a riverine habitat in southern Africa (Shamvura stretch of the Okavango River). In total, 84 waterfowl species were recorded. The birds were assigned to different guilds according to their migration activity, diet and nesting site selection. In overall, the species number was almost the same (74 vs. 73) in the wet and dry season. The abundance of all resident species recorded was lower in wet (N = 5992) than in dry seasons (N = 6965)(χ² = 73.1, P < 0.01). In both seasons Palearctic migrants were represented by seven species, which comprised 1–2% of all waterbirds. Six species were classified as dominants: African reed cormorant Phalacrocorax africanus, African openbill stork Anastomus lamelligerus, cattle egret Bubulcus ibis, wattled lapwing Vanellus senegallus, African darter Anhinga rufa and white-faced duck Dendrocygna viduata. In the wet season the dominant species comprised 68%, while in dry season – 52.5% of all birds recorded. Significant seasonal differences in the numbers of individuals were shown for the following species: African reed cormorant, great egret, squacco heron, wattled lapwing and pied kingfisher. Insectivorous and omnivorous birds were more abundant in wet season, while piscivorous, carnivorous and plant eating birds in dry season. These differences can be related mainly to seasonal variation in the availability of food as well as to the timing of breeding.