Given the significant initial investment and long life span of road-stream crossing structures, interest has grown in developing tools to evaluate their physical and biological effectiveness. In this case, the physical effectiveness monitoring guidelines being developed consist of two protocols; Level 2 is a detailed, statistically-based survey and evaluation of a suite of physical habitat metrics, while Level 1 is a simplified subset of that. Our premise for both monitoring protocols is that if the design channel characteristics through the crossing are similar to a nearby representative reach of the natural channel, then the design channel is considered to be effectively providing geomorphic, hydrologic, and ecological continuity that ultimately benefit fish and other aquatic organism passage. The first step for level 2 monitoring is selecting a representative reach in the natural channel that is most similar in gradient, length, and channel type as the design channel through the crossing using a surveyed longitudinal profile. A suite of channel metrics are then measured and statistically evaluated along the length of the representative reach, design channel, inlet transition, and outlet transition. Channel metrics measured and analyzed include 1) channel width at bankfull flow, half of bankfull flow, and low flow; 2) bank margin irregularity at bankfull flow, half of bankfull flow, and low flow, 3) maximum residual flow depth, 4) lateral bed variability, and 5) bed-material particle-size distributions and different percentile particle sizes. We use the multiple response permutation procedure and non-parametric derived confidence intervals for the various channel metrics in the design channel, inlet transition, and outlet transition to determine if they are similar or different than those in the representative channel. These results from the different channel metrics are weighted and integrated in a summary rubric to develop an overall score for physical effectiveness. Because of the time needed to collect, analyze, and interpret the data from level 2 physical monitoring, it is intended to be applied only at a subset of sites to gain a better and more complete understanding of road-stream crossing channel design methods and overall physical effectiveness.