Several non-native trematodes hosted by the invasive Eurasian faucet snail, Bithynia tentaculata, have been causing die-offs of waterfowl in the Midwestern United States and Canada for several decades. Because of the potential implications of these die-offs on waterfowl in non-native settings, it is necessary to better understand the trematodes that cause the die-offs. Here, we studied the spatio-temporal dynamics of two trematodes, Cyathocotyle bushiensis and Sphaeridiotrema spp., known to infect waterfowl in northern Minnesota, USA, via their intermediate host, the faucet snail (Bithynia tentaculata). We studied prevalence (% of snails infected within a sample) and intensity (mean number of parasites per infected snail within a sample) of faucet snail infection with these two trematodes in small lakes, large lakes, ponds, and rivers in northern Minnesota in the spring, summer, and fall of 2011–2013. We tested whether parasite prevalence and infection intensity could be explained spatially (as a function of the abundance of faucet snails, average snail size, water depth, and proximity to known waterfowl groups) and temporally (across years and seasons) using generalized estimating equation models. The spatial and temporal patterns we observed varied within and among waterbodies. For both parasite species, parasite prevalence and intensity of infection were consistently higher in samples with larger snails and in deeper portions of the waterbodies. In Lake Winnibigoshish, prevalence was lower farther from the large waterfowl groups we observed, but the abundance of snails in a sample had no effect on prevalence or intensity of infection. Our findings help improve understanding of this multi-species system, but also illustrate the complexity of modeling the spatial and temporal dynamics of infections in waterbodies that are so variable in size, shape, waterfowl use, and function.