Understanding the niches of intermediate hosts and vectors for environmentally transmitted pathogens is crucial for identifying endemic areas, assessing habitat suitability and targeting interventions. This study focuses on intermediate hosts of intestinal schistosomes, with over 700 million people at risk of lifelong infection. We compared habitat suitability and species interactions across 674 sites in 52 villages in rural Uganda between 2022 and 2024, capturing a severe flooding event. Spatiotemporal models incorporating a polygon-based method to account for space with time as a fixed effect were developed to analyse snail abundance for Biomphalaria sudanica and B. stanleyi. B. sudanica was associated with marshy sites near lake shorelines and presence of hyacinths, while B. stanleyi was more likely to be found in deeper waters with Vallisneria plants. However, cohabitation was common for both species. Habitat suitability for each species fluctuated temporally, and more starkly with extreme flooding, resulting in switching of species dominance. Our study suggests that events consistent with climate change may influence habitat suitability without necessitating an expansion of environmental areas. Our models enable tracking of dynamic ecological niches that, if replicated elsewhere and for other intermediate hosts or vectors, can be used to better target environmental and community interventions as environmental conditions change.