Water quality
The Reserve is working with local shellfish hatcheries to monitor for harmful algal blooms.  Changing climatic conditions have been associated with increased Harmful Algal Blooms [HAB] in coastal waters. These blooms can cause detrimental impacts on the local ecosystem in addition to causing Paralytic Shellfish Poisoning in humans.  In an effort to educate oyster farmers and local citizens on HAB awareness and monitoring, the Reserve partnered with the Phytoplankton Monitoring Network, the University of Alaska Fairbanks, the University of Alaska Southeast, and the Northwest Fisheries Science Center to deliver a HAB workshop.  This workshop enabled participants to determine species composition and distribution of harmful and potentially toxic phytoplankton in local waters and additionally helped participants develop an understanding of the impacts of HAB on the environment and human health.  As a result of this workshop, multiple volunteers are now monitoring Reserve waters for potentially toxic phytoplankton. As part of this effort, community monitors throughout Kachemak Bay deployed Tidbit water temperature sensors for monitoring the variability of water temperatures throughout various sub-bays.  During the summer reporting period the Reserve supplied temperature sensors that were deployed by community monitors in Jackolof Bay, Peterson Bay, Halibut Cove, and Bear Cove. Data is returned to monitors on a monthly basis and reported to the Alaska Department of Conservation.

The value of ongoing monitoring was demonstrated in the summer of 2009 when the Reserve assisted in determining the cause of a large hatchery release die-off on June 3rd.  About 60% of hatchery-reared silver salmon smolt, approximately 64,000 fish, died mysteriously shortly after their release into Homer’s fishing lagoon.  Hatchery staff questioned their rearing and release methods until laboratory analysis revealed that the die-off was the result of a plankton bloom of chaetocerous diatoms.  Hungry smolt unwittingly ate the abundant diatoms which have sharp projections that cut the fish gills and cause suffocation due to mucus secretion in reaction to the abrasions. The Reserve's monitoring of several sites in the bay indicated high levels of chaetocerous diatoms since late May.  

Changes in Biological Communities
Beginning in 2005, the Reserve's research and education staff worked together to design a scientific protocol for invasive monitoring of green crabs, as well as curriculum, monitoring kits, and data sheets. The program was successfully launched at local schools in the Homer area. In 2007, the Reserve received NISA funds to expand the monitoring program into the neighboring communities and the villages of Port Graham, Nanwalek, and Seldovia.  This successful program has multiple monitoring sites throughout the bay with plans for expansion into classrooms on the Kenai Peninsula and Prince William Sound. The monitoring teams include students, native organizations, and local community members. Expanding the green crab monitoring program throughout the inlet allows the Research Reserve a greater source of early detection for potential crab invasions and helps to establish baseline population information on native crab populations in Kachemak Bay.  To date no invasive green crabs have been identified in Alaskan waters.
In addition to Green Crab monitoring, the Reserve has taken a leadership role in monitoring for invasive tunicates. As a regional coordinator, the Reserve distributes, manages, and provides support for plate monitoring sites throughout Southcentral Alaska. In 2007, the Reserve contracted the Smithsonian Environmental Research Center (SERC) to conduct multiple workshops aimed at (a) identification of non-native species and taxonomic training and (b) strategic planning for detection and monitoring and broader-scale regional partnerships. Reserve staff were trained at identification, and a taxonomic reference collection of photos and preserved specimens of the most likely marine invasive species was contracted by SERC. These species were collected, photographed and preserved. They are now housed at the Reserve. The Reserve is positioned to be a leader in coordination and local expertise in identification and monitoring of these species.

Habitat Alteration
Headwater streams are the uppermost reaches of watersheds, and while they are small in size, they provide important habitat for juvenile salmon on the lower Kenai Peninsula. These headwater rearing habitats, however, are often overlooked by existing management approaches because they tend to be farther from existing access, physically located beyond the stream reaches that adults use for reproduction, and so little is known about them. The Reserve's staff are  providing  new data on habitat requirements for the early life stages of juvenile salmon and provides management with a preliminary model for identifying important salmonid habitat in headwater streams.  The work provides important information for habitat protection to inform watershed-based management plans and guiding decisions about land-use requests.

The largest estuary in Kachemak Bay is the combined Fox River and Sheep Creek estuary, located at the head of the Bay.  The Fox and Sheep rivers have their origins in glaciers within the Kenai National Wildlife Refuge, and flow out into the large estuary complex, known as the Fox River Flats, which was designated as a state Critical Habitat Area in 1972.  Due to the remoteness, little research has been conducted on how fish and wildlife use this area. This year, Reserve researchers began to fill this information gap by investigating how juvenile salmon use this estuary as they migrate from freshwater to the sea, which biologists call ‘out-migration’.