The Ecosystems Investigations Program (EIP) has three basic research functions: biological surveys, water quality monitoring/assessment, and interdisciplinary watershed studies. Investigations by Survey biologists in the past documented the habitats and distributions of fishes in the Mobile-Tensaw River Delta and the Tennessee, Cahaba, lower Tombigbee, and Black Warrior River systems; in the Gilbertown, Pollard, and Citronelle oil field areas; and in streams draining the Warrior coalfield. For about a decade in the late 1990s the EIP was also actively involved in documenting the movements of large riverine fishes, such as the Southeastern Blue Sucker, Smallmouth Buffalo, Paddlefish, and Gulf Sturgeon. Those studies led to a better understanding of how fishes utilize rivers throughout the year and will assist state and federal conservation agencies and river management agencies to better fulfill their water resources mandates and obligations. Investigating Alabama's rich mussel fauna began in 1992 and continued for about 25 years, updating information on the faunas of each major river basin in the state, including the Alabama, Chattahoochee, Choctawhatchee, Conecuh, Tennessee, and Tombigbee Rivers, and provided the information necessary to guide the creation of Strategic Habitat Units (SHUs) for habitat restoration and species reintroduction efforts currently underway. The Survey maintains small reference collections of fishes, mussels, crayfishes, and aquatic insects that are available for scientific use or public tour. Most of the invertebrate collection was transferred to the Auburn University Museum of Natural History and the fish collection was transferred to the University of Alabama Ichthyological Collection, making that collection one of the largest of its type in the southeast. The crayfish collection is set to be transferred to the University of Alabama Decapod Collection soon. During the early period of mussel research material was donated to The Ohio State University Museum of Biological Diversity and a few smaller museums, but most of the mussel collection was donated to the North Carolina Museum of Natural Science for use in the book Freshwater Mussels of Alabama and the Mobile Basin, published in 2008. More recently Survey biologists assisted in developing distribution information on the relatively unknown crayfish fauna of the state through field collecting and producing species distribution and habitat maps, ultimately leading to the comprehensive book Crayfishes of Alabama.

Crayfishes of Alabama, a 496-page book summarizing the state’s crayfish fauna, was published in April 2022. After a cumulative 49 years of research and writing in collaboration with Dr. Guenter A. Schuster, retired Professor Emeritus from Eastern Kentucky University, and Dr. Christopher A. Taylor, Principal Research Scientist and Curator of Fishes and Crustaceans in the Prairie Research Institute of the Illinois Natural History Survey, staff of the Ecosystems Investigations Program co-authored the book, which is the first comprehensive book on the crayfish fauna of the state. It was published by the University of Alabama Press and complements earlier publications defining other major faunal groups in our remarkably diverse waterscape, including fishes (Mettee and others, 1996; Boschung and Mayden, 2004) and mussels (Williams and others, 2008). The book is a significant contribution to the science of crayfishes, as Alabama has more species than any other state, with 100 recognized to date, about 1/4 of the list of crayfishes in North America and 1/6 worldwide. Many of the species are endemic to the state, several others are found only in Alabama and one or a few adjacent states, and many in numerous other states as far north as Canada and west to the Rocky Mountains. Others have been spread by anthropogenic means as far west as California and Hawai’i, and even internationally. The book was based on considerable research into historic records from as far back as 1853, gleaned from countless hours visiting significant museum and university collections and compiling those records into a searchable, georeferenced database. That initial dataset was complemented by thousands of records secured by the authors and a host of willing associates from 2005 up until literally months before publication. Samples were collected broadly across the state, filling in data coverage and habitat gaps based on the historical record, and using means appropriate in the collection area, whether that be by hand-digging, use of baited traps, dipnets and seines, or by hand picking in shallow water. The book includes plates of color photographs of whole animals and key characters, a photographic key, dot distribution maps with physiography and stream bases highlighted, in-depth species accounts, descriptions of morphological characters, crayfish associates, distributions of species across the state and among different habitats, conservation statuses, etc. Research for the book was supported by grants from ADCNR through funds provided by the State Wildlife Grants program and Section 6 of the Endangered Species Act, USFWS, and GSA.

The Ecosystems Investigations Program has also been actively involved in documenting the movements of large riverine fishes in Alabama, such as the southeastern blue sucker, smallmouth buffalo, paddlefish, and Gulf sturgeon. These studies have led to a better understanding of how fishes utilize rivers throughout the year and will assist state and federal conservation agencies and river management agencies to better fulfill their water resources mandates and obligations.

Survey biologists have worked closely with biologists of the Alabama Department of Environmental Management (ADEM) and ADCNR to develop a standardized fish community sampling protocol and statewide analysis tool for evaluating stream biological condition. This tool will be invaluable for evaluating stream water quality and providing biological justification to water quality management decisions. Additionally, the EIP recently partnered with the U.S. Fish and Wildlife Service (USFWS), Cawaco RC&D, and ADCNR to focus on recovery and restoration of rare aquatic animals through a process known as the Strategic Habitat Initiative, which led to the development of the SHU concept. Bringing watershed stakeholders and partners together to improve aquatic habitat and water quality cooperatively will be a significant part of how water resources will be managed and protected in the future, and the Ecosystems Investigation Program is helping to put this process into effect.