Since 2004, Balance Hydrologics (Balance) has assisted the City of Santa Cruz, in cooperation with other project team members prepare a Habitat Conservation Plan (HCP) for the watersheds from which the community draws its water supply. Balance has and is presently leading HCP efforts focused on (1) hydrologic characterization of watersheds which provide drinking water through diversions at run-of-the-river dams, (2) development of a custom-built MATLAB model framework to evaluate how diversion operations interact with water supply demand and the quality of downstream steelhead (Oncorhynchus mykiss), and (3) development of a custom-built hydrologic model to evaluate how climate change predictions in air temperature and rainfall for three different emissions scenarios may affect water supply availability, and the quality of steelhead habitat under future conditions. Our involvement and work on the HCP is founded on a comprehensive field-conditions monitoring program that has provided our model applications with 6 years of data representative of real conditions under a variety of climatic conditions. A draft of the HCP document has been submitted to the regulatory agencies, and negotiations are presently underway to finalize new regulatory permits to continue operation of water supply sources for the benefit of the community as well as steelhead and other aquatic organisms.