Fishes are among the most imperiled classes of vertebrate animals, with approximately 39% of North American fish species exhibiting population declines and extinction risk. Headwater stream fish assemblages are comprised of unique assemblages of headwater specialists, adaptable generalists, and imperiled species. These assemblages are of particular interest in the Midwestern United States given the high rates of modification and degradation of headwater streams in that region. In addition to supporting their own diverse communities, headwater streams are also ecologically important due to their strong influence on downstream water quality. Many studies have previously examined how hydrology, water chemistry, landscape modification, and climate affect stream fish communities in the Midwest. However, relatively few studies have examined relationships between those environmental metrics and individual species. To address this knowledge gap, we performed occupancy modeling using fish captures and instream habitat surveys from 14 years of electrofishing surveys in the Cedar Creek watershed, Indiana and East Branch of the Saint Joseph River, Michigan. Specifically, we sought to broadly describe occupancy trends, quantify occupancy drivers for each species, and identify differences in drivers between species and the overall community. We identified over 64,000 individual fish and 39 unique species, retaining 31 species for modeling. Latent occupancy probability increased for 13 species, decreased for six species, and was roughly stable for nine species. We examined four sets of environmental covariates: water chemistry, hydrology, substrate, and instream vegetative cover. Stream depth and width were the most important drivers of occupancy for most species, although water temperature and conductivity were also important for some species. A few species also showed strong distinctions between their occupancy drivers and those of the overall community, such as conductivity, dissolved oxygen, and temperature for blacknose dace and silverjaw minnow. Our results emphasize the importance of considering the needs of individual species when making conservation decisions and suggest a one-size-fits-all management plans are likely inadequate to maintain diverse headwater stream fish assemblages.