Freshwater river mouths are transitional habitats at the interface of where tributaries meet large lakes. Here we focus on drowned river mouths (DRMs), which are protected, lake-like ecosystems that connect tributaries to Lake Michigan, USA. We show that DRMs are more eutrophic than Lake Michigan and provide evidence of a latitudinal environmental gradient along eastern Lake Michigan, with more eutrophic conditions in the south. Moreover, we show that seasonal thermal stratification in the water column is common during summer in DRMs that are sufficiently deep. Thermal stratification is often associated with low dissolved oxygen concentrations in the hypolimnion, which likely affects the spatial distribution of fishes. We show that DRMs are used by a diverse assemblage of fishes and focus on Yellow Perch Perca flavescens, which exhibit both resident and migrant life histories. Residents primarily use one habitat (i.e., DRM or Lake Michigan), whereas migrants move between habitats. Lake Michigan migrant Yellow Perch seasonally move from Lake Michigan to DRMs during winter when DRMs are not thermally stratified, although many details on the timing and periodicity remain unclear. In conclusion, DRMs are an important habitat in eastern Lake Michigan that are used by both migratory and resident fishes.