Section 4. 
Implementation Plan for Habitat Alteration Research 
Problem 
Significant improvements in some aspects of the North American environment have been 
realized over the past several decades, but the continuing increase in human populations and 
associated activities has created an array of regulatory and policy challenges (e.g., land-use 
changes, hydrologic modification, climate change, altered biological diversity, introduction of 
normative species, concern about ecological sustainability, and cumulative effects of manmade 
chemicals) that defy traditional command/control approaches (EPA 1999). Many anthropogenic 
activities exert their influence on biota via effects on habitat, and habitat alteration is arguably 
the most important cause of declines in ecological resources in North America (EPA 1990). 
Thriving populations of fish, shellfish, and wildlife are valued by the public, not only for 
commercial, recreational, and aesthetic reasons, but also as tangible and visible surrogates for the 
overall condition of the environment. Habitats essential to the well being of these species are 
rapidly being affected by a myriad of land-use activities. Habitat alterations have been identified 
as a major cause of endangerment for species within the United States. For example, the U.S. 
has the most diverse temperate freshwater fish fauna in the world, but 35-40% of its 790 fish 
species are imperiled because of poor land use practices, wetland alteration, introductions of 
exotic species, and other habitat-altering factors (Warren and Burr 1994, Stein and Flack 1997). 
EPA has not traditionally focused its research, regulatory, or policy effort on habitat alteration. 
However, a number of factors converge to justify a new EPA emphasis on habitat issues. The 
CWA has a goal "to restore and maintain the physical, chemical, and biological integrity of the 
Nation’s waters," including the "protection and propagation of fish, shellfish, and wildlife." 
While the chemical integrity of aquatic resources is much improved, physical and biological 
integrity remains a concern. Habitat alteration is a common cause for the failure of aquatic 
systems to meet designated uses as required by the CWA, and addressing these failures 
increasingly requires ameliorating the cumulative impacts of diffuse stressors including nutrient 
loading, sedimentation, and altered hydrologic regime. The necessary integrated approach to 
environmental protection is perhaps best provided by habitat-based criteria. As required by the 
Endangered Species Act (ESA), EPA is increasingly being asked to participate in interagency 
species protection and restoration efforts where habitat issues play a key role. Because one of 
EPA’s core ecological regulatory authorities is the CWA, the species endpoints for which habitat 
alteration is of greatest concern are aquatic species (i.e., fish and shellfish), and water- and 
wetland-dependent wildlife. By focusing on aquatic ecosystems and habitats supporting species 
of combined ecological and societal importance, EPA can advance broad environmental 
protection goals while directly addressing issue-driven stakeholder concerns. 
EPA’s Office of Water (OW) has identified priority ecosystem types for which habitat alteration 
research is especially needed. These systems include freshwater and estuarine wetlands, stream 
corridors, and marine and Great Lakes coastal zones. Not coincidentally, these resource types are 
of considerable importance in sustaining ecologically and societally valuable fish, shellfish, and 
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