In 2004 BIO-WEST began working on the Matagorda Bay Health Evaluation, a collaborative project that involved a team of private, local, and state entities to study the importance of freshwater inflow to the Matagorda Bay system. Located on the Texas coast near Houston, the Matagorda Bay system is characterized by large changes in salinity over a broad range of temporal and spatial scales. The aquatic environment ranges from large expanses of shallow, non-vegetated bay bottom to seagrass beds and oyster reefs, to fringe marshes around the bay. The Colorado River flows into the eastern arm of Matagorda Bay, providing a developing delta at the mouth of the river with freshwater, nutrients, and sediment. For over two years BIO-WEST studied baseline environmental conditions within the bay and relationship development between key aquatic species and habitat based on biological, chemical, and physical variables such as freshwater inflow, salinity, temperature, inundation regime, physical features and/or substrate type, and organism abundance. We also participated in the evaluation of the bay’s health and productivity using a hydrodynamic/salinity model to key species biological responses or suitability indices. These species include brown shrimp (Farfantepenaeus aztecus), white shrimp (Litopenaeus setiferus), blue crab (Callinectes sapidus), eastern oyster (Crassostrea virginica), Atlantic croaker (Micropogonias undulates), and Gulf menhaden (Brevoortia patronus), as well as primary production in the form of coastal wetlands (low and high intermediate and estuarine marsh). Additionally, we conducted a series of sampling events in Matagorda Bay and East Matagorda Bay to evaluate seasonal marsh productivity and provide additional data on use of shallow-water habitats by key project species. Each sampling effort involved measuring water quality, identifying and measuring wetland plant species, and collecting fish and crustaceans using a modified throw-trap technique in several regions of the bay. Because oyster reefs serve as important aquatic habitat and oysters are a commercially important species for harvest, their importance to the bay is unique. We evaluated oyster conditions in the bay, mapped previously undocumented oyster reefs, and conducted field studies to acquire data on oyster size and population, as well as parasite infestation levels of various oyster reefs and their relationship to freshwater inflow.