Stock-recruit (SR) relationships have been reported for numerous stocks of trout and Pacific salmon, but despite the intuitive appeal, evidence of such relationships is lacking for brook trout (Salvelinus fontinalis). The relationship between number of adults spawning in a stream and the subsequent number of young produced can be used by management to predict year class strength. Disruptions of SR relationships (for species that exhibit strong relationships) can be indicative of environmental perturbations or habitat impairment. As part of a long-term study we have estimated brook trout abundance and measured habitat and water quality in 25 headwater streams in West Virginia since 2003. These streams span 4 geologies and include: Hampshire group, Mauch Chunk, Chemung, Pottsville, and Pottsville streams limed by the West Virginia Department of Environmental Protection. Strong SR relationships were detected for streams in the Hampshire group (P < 0.01) and the Pottsville group (P < 0.05). The relationship differed among years within the Hampshire groups suggesting the influence of annual variation in conditions such as stream discharge in structuring brook trout populations. Analysis aimed at identifying stream features (habitat, water quality, elevation, gradient, benthic macroinvertebrate community metrics, etc.) failed to detect any consistent variable related to strength of SR relationships in the streams. Although we were able to find a SR relationship for brook trout in some geologies, we were unable to find significant explanatory variables correlated with the relationship. This is likely due to different factors or combinations of factors weakening the underlying SR relationship in different streams. Further elucidation of factors affecting SR relationships will be possible with continued sampling of these streams.