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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. 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. 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 north‐eastern Indiana and southern Michigan, U.S.A. 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. 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.
