Limited information is known regarding the rotifer community on the Upper Mississippi River (UMR). Studies have shown that rotifers are a common prey for invasive bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) as well as native fishes of the UMR and there is concern these invasive carp will compete with native fishes for food resources. This study was conducted to provide baseline rotifer community data before range expansion of these invasive carps into the upper reaches of the UMR. Vertical tows were taken to collect rotifer samples over a four year period in Lake Pepin, a natural riverine lake in Pool 4 of the UMR. Four dominant genera (Keratella, Polyarthra, Trichocerca and Brachionus) comprised the samples and significant correlations between rotifer abundance and temperature, volatile suspended solids and chlorophyll-a were observed. Our results identify potential drivers of rotifer abundance and provide robust rotifer abundance and composition data. These pre-invasion data are critical to recognizing the effects invasive carp have on zooplankton communities and the UMR ecosystem.