Most northeastern river basins are stressed by the effects of development but the complexity of evaluating rivers often hinders the establishment of effective management regulations. Many methodologies have been proposed for assessing instream habitat, determining critical flow levels, and evaluating biological communities, but no one approach is universal. The overall objective of this thesis is to move towards standardizing components of river modeling. Rather than examine a full model, I investigated individual steps of MesoHABSIM, an instream habitat modeling approach. The two components studied involved applying the Reference Fish Community (RFC) method to identify a biological reference; and using depth and velocity data to standardize the description of hydraulic types. The RFC approach identifies the fish species and the expected proportions that should be present in a less impacted version of a river system. The Eightmile River watershed, was the focus of the study in which the RFC approach was employed to determine whether the fish community of this rural watershed, meets or exceeds a community developed using reference rivers. Similarity indices were used to identify differences between the existing (field-sampled) and expected communities. While the analysis of the Eightmile community indicates that it is in a better condition than the majority of rivers studied, it also shows some deviation from the reference, most likely due to elevated water temperatures and regional declines. The hydraulic type characterization study was developed to reduce the effort needed in depth and velocity measurement after this was identified as the most time consuming portion of the MesoHABSIM methodology. I used a series of pair-wise, independent-sample, Kolmogorov-Smirnov tests on a large bank of depth and velocity data to determine if patterns could be confirmed for each type of hydromorphological unit (HMU) across various streamflows. Few of the data sets were statistically similar enough to be combined and the mapping effort could not be simplified based on this investigation. Neither investigation provided the intended reference for the particular component of river modeling, further emphasizing the complexity in this area of study. However, the information gathered can be used as pioneering steps in future investigations.