Channelized agricultural headwater streams are common throughout agricultural watersheds in the midwestern United States. Understanding fish-habitat relationships within these streams will provide information that can assist with developing conservation and restoration strategies for these degraded streams. From spring 2006 to fall 2010, we collected fishes and measured riparian habitat, instream habitat, and water chemistry variables from seven sites in Cedar Creek, Indiana, and 14 sites in Upper Big Walnut Creek, Ohio. We found that fish community structure was more strongly correlated with instream habitat than riparian habitat or water chemistry in both watersheds. We also observed interrelationships among instream habitat, watershed size, and fish communities within both watersheds that suggest that the hydrological changes that occur with increasing watershed size are the underlying factor for fish community changes that occur with increasing watershed size. Our results suggest that conservation and restoration efforts within channelized agricultural headwater streams in the midwestern United States, where nutrients and herbicide concentrations are low, need to address physical habitat degradation to positively influence fish community structure.

1. Conversion of land for agriculture has led to the channelisation of headwater streams and reduced water quality. Resident fish populations are expected to be challenged under such conditions and may experience declines that lead to a loss of neutral genetic variation. 2. However, species-specific responses to recent ecological changes in stream condition and/or range expansion following glacial retreat can also influence the pattern of genetic variation found within and among contemporary populations. To evaluate the relative roles of contemporary and ancient scenarios that are hypothesised to affect the genetics of populations in streams, we studied the creek chub (Semotilus atromaculatus), a common species that is tolerant of stream degradation. 3. We screened eight microsatellite loci on 308 individuals originating from ditches and streams surrounded by agricultural and forested land cover within the St. Joseph River catchment in northeastern Indiana and southern Michigan, U.S.A. 4. We found weak population structure associated with land cover and, in contrast to expectation, higher allelic richness in agricultural streams. Using Bayesian coalescent modelling, the strongest pattern found within the data set was evidence of a population decline throughout the catchment that most likely preceded stream channelisation and land conversion. 5. The results illustrate the complexity of using neutral genetic variation of populations to assay stream quality. Tolerant species may have increased gene flow in channelised streams that leads to an increase in genetic variation. Meanwhile, post-glacial landscape change and subsequent colonisation of nascent freshwater streams appears to shape genetic variation regardless of contemporary land use.