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We studied waterfowl abundance and diversity in relation to season (wet vs dry), wetland characteristics (vegetation and morphometrics) and land-use in a semi-arid agricultural region of South Africa to determine how waterfowl respond to various wetland characteristics, particularly those of permanent agricultural ponds. Wetlands were visited during the wet (n = 215) and dry (n = 178) seasons of 1997 and species’ abundances, and wetland and upland characteristics were recorded. Canonical correspondence analyses and multiple regressions determined which wetland and upland characteristics were most strongly associated with waterfowl density and species richness for both the wet and dry season. Overall, diving ducks were not abundant in the wet season, and were rare to absent in the dry season. Divers only responded positively to the characteristics of natural wetlands, including greater surface area, percent coverage of emergent vegetation, and high (ungrazed) shoreline vegetation. Of six species of dabbling ducks present during the wet season, occurrence of three co-varied with wetland and upland characteristics associated with agriculture, namely permanent water, and agricultural grains in the dry season. Being largely grazers, geese responded positively to the higher proportions of bare shoreline, characteristically surrounding agricultural ponds. Because only a few species associated with artificial waterbodies, natural wetlands should be conserved to protect waterfowl diversity in semi-arid South Africa.