Impacts of low-water crossings on aquatic resources under the United States Army Corps of Engineers Nationwide Permit (NWP) Program

The U.S. Army Corps of Engineers is charged with the responsibility of enforcing section 404 of the Clean Water Act (CWA). In order to improve the efficiency of permitting, Congress has authorized a set of Nationwide Permits (NWP), which are activities authorized by Congress so long as certain project-specific minimal impact thresholds are met. Activities authorized by NWPs are expected to produce minimal effects, both individually and cumulatively, to the aquatic environment. This dissertation explores a frequent criticism of the NWP program: that the Corps' program fails to account for indirect effects of its permit decisions, where an indirect effect is a downstream, localized impact not accounted for in the project-specific authorization.; A focused study was employed to evaluate the temporal effects of LWCs on a single set of crossings on the Santa Ynez River in the Los Padres National Forest following storm events for two consecutive water years (2002--2003 and 2003--2004). Data reveal that rainfall induces both scour and fill below LWCs in the Santa Ynez River. A spatial survey of forty-one crossings in the Santa Clara River watershed using a high-resolution mapping GPS in conjunction with a GIS database was useful to explore first the generality of potentially observed indirect effects. The data indicate both scour and fill below LWCs is ubiquitous in the watershed region studies. Furthermore, various design features of the crossings---hard vs. soft; at grade vs. above-grade; culvert vs. no culvert---are correlated with observed indirect effects, most likely due to hydrologic issues associated with the design features. A seine-net approach was utilized to connect potential ecological effects due to changes in river geomorphology in the Santa Ynez River. Seine netting above and below the LWCs shows that aquatic species assemblages are statistically more abundant below crossings, as well as richer and more diverse. Results of this dissertation indicate that the Corps NWP program does indeed fail to account for the indirect effects of at least one of its authorized NWP programs---NWP 14 for linear transportation crossings---and these indirect effects include changes in river morphology, species assemblages, and potential effects to endangered species.