We evaluated changes in wetland abundance, size, and classification between average (1979–1986) and above-average (1995–1999) precipitation periods for two physiographic regions in eastern South Dakota. Temporal shifts in wetland numbers, area, and class varied by topographic location. In high wetland density areas (> 8 wetlands/100 ha), our data suggests that larger, semipermanent wetlands expanded and absorbed nearby wetland basins into their margins, resulting in a net “loss” or disappearance of temporary and seasonal wetlands in above-average water condition years. “Losses” described here are not deemed permanent as in cases of draining or filling, and wetlands may re-form when water conditions return to normal. Nevertheless, temporary disappearance of smaller more isolated wetlands may have implications for breeding waterfowl and other fauna. Percent change of semipermanent basin numbers was positively correlated with wetland density, whereas the opposite was true for seasonal wetlands. Loss of temporary wetlands was correlated with wetland aggregation within the sample area. However, in low wetland density areas, the number and size of seasonal and temporary wetlands generally increased following above-average precipitation. We suggest that wetlands' spatial arrangement be considered along with traditional wetland quantification techniques to better account for shifts in wetland habitat in dry versus wet years.