Arizona Wildlife Conservation Strategy

Lotic Systems

Lotic ecosystems have flowing water that can be perennial, intermittent, or ephemeral (Zaines 2007). These systems include associated riparian corridors and connecting ephemeral channels. In Arizona, lotic systems range in size, from the large, free-flowing Colorado River to small stream channels that only contain water following rain events. All of these lotic systems are extremely fragile and provide important habitat for native fish, birds, aquatic organisms, and other riparian-dependent wildlife species (Bunn et al. 2007).

The Colorado River is Arizona’s largest river, with an annual discharge that ranks 25th largest in the United States (lseri and Langbein 1974). Meanwhile, the Gila, Salt, and Verde — which are considered large rivers for Arizona — have discharges considerably less than the Colorado. Arizona’s moderate-sized rivers include the San Pedro, Santa Cruz, Little Colorado, White, Black, Blue, San Francisco, Bill Williams, Agua Fria, and Babocomari. Additionally, there are hundreds of smaller perennial, intermittent, and ephemeral streams that are tributaries to these larger systems (Goodrich et al. 2018).

Geology and hydrology shape lotic systems through fluvial processes, or the interaction between flowing water and the river channel (Hereford 1984). These interactions create a variety of macro- and microhabitat types, including cascades, riffles, runs, glides, pools, and others. Aquatic wildlife and organisms inhabit these macro- and micro-habitats depending on their adaptations (Wood and Bain 1995).

Arizona has a bimodal pattern of annual precipitation that drives these fluvial processes. Intense but short-term precipitation during the summer often results in localized flash floods, making lotic systems turbid with suspended sediments (Graf et al. 1981). Native aquatic wildlife are adapted to these rapid changes in flows and turbidity (Brouder 2001). Conversely, winter precipitation can be less intense and more prolonged, providing opportunity for interconnectedness between perennial reaches that are otherwise disconnected during drier periods (Jager et al. 2014).

Lotic systems in Arizona are occupied by a variety of algae and submerged aquatic plants that form the base of the food web while also providing habitat for aquatic invertebrates and vertebrates. The biomass of algae and submersed plants in lotic systems is highly dependent upon the amount of sunlight reaching the stream, which is affected by the geologic setting, riparian vegetation, and suspended sediments (Bunn et al. 2006).

Primary threats affecting lotic systems include drying, sedimentation, non-native species, and pollution (Stromberg and Tellman 2009). Drought, climate change, water diversions, and groundwater pumping contribute to stream drying, resulting in habitat loss and reduced diversity of aquatic wildlife (Rinne et al. 2005). Sedimentation is caused by overgrazing, timber harvest, excessive OHV use, runoff from roadways, and precipitation events following wildfire. The spread and invasion of non-native species can also alter the native lotic community composition, replacing some assemblages entirely and increasing degradation of native riparian habitats (Olden and Poff 2005). Finally, pollution is a much more localized stressor to lotic systems. Effluent from mines, agriculture, and urban areas can transport a variety of pollutants that can severely degrade lotic communities (Singh 2010; Dolan and Mannan 2009).

All of these stressors can disrupt lotic food webs and negatively-affect aquatic wildlife (Tellman et al. 2009). A focused and collective effort is necessary to reduce these threats where possible, conserve and protect the remaining functioning lotic systems, and restore riparian habitat in key areas where species benefit is maximized.

Significant Habitat Features

The following describes habitat features or microhabitats that are unique to lotic systems and are of particular importance to certain species:

  • Low-gradient riffles with pebbles and cobbles that are not embedded in fine substrates are required for loach minnow which lay eggs on the underside of these rocks (Propst and Bestgen 1991).

  • Edgewaters below riffles and cascades are important for spikedace where they school and feed on drifting insects (Rinne 1991).

  • Sand to gravel sized substrates are needed for spawning habitat for Gila trout, Apache trout, spikedace, speckled dace, longfin dace, chub species, and all of the native suckers (Rinne 2001; Minckley and Marsh 2009).

  • Apache and Gila trout prefer non-turbid streams with a mix of pools and riffles that have instream and overhead cover, as well as larger sediments that are not embedded (Cantrell et al. 2005).

  • Apache and Gila trout generally require mean daily water temperatures of less than 68℉ (20℃) year-round (Lee and Rinne 1980; Petre and Bonar 2017).

  • Large- and moderate-sized connected rivers are preferred by many of the big river fish species, including razorback sucker, Colorado River pikeminnow, flannelmouth sucker, and bonytail, where they can complete their reproductive cycles and migrate up and down the river corridors. However, these habitat types no longer exist within Arizona due to damming of rivers (Minckley and Marsh 2009).

Strategy Species

The following list represents SGCN in this habitat type that AZGFD actively manages or are watching closely due to some level of concern:


Arizona Toad, Chiricahua Leopard Frog, Lowland Leopard Frog, Northern Leopard Frog, Relict Leopard Frog, Tarahumara Frog


Abert's Towhee, American Dipper, Bald Eagle, California Black Rail, Bullock's Oriole, Elegant Trogon, Golden Eagle, Hooded Oriole, Western Least Bittern, MacGillivray's Warbler, Osprey, Painted Redstart, American Peregrine Falcon, Southwestern Willow Flycatcher, Western Yellow-billed Cuckoo, Ridgway's Rail


Apache Trout, Beautiful Shiner, Zuni Bluehead Sucker, Bonytail Chub, Colorado Pikeminnow, Desert Pupfish, Desert Sucker, Flannelmouth Sucker, Gila Chub, Gila Topminnow, Gila Trout, Humpback Chub, Little Colorado Spinedace, Little Colorado Sucker, Loach Minnow, Longfin Dace, Mexican Stoneroller, Sonoyta Pupfish, Razorback Sucker, Roundtail Chub, Sonora Chub, Sonora Sucker, Spikedace, Virgin River Chub, Woundfin, Yaqui Catfish, Yaqui Chub, Yaqui Sucker, Yaqui Topminnow


California Floater


New Mexican Jumping Mouse, Western Red Bat


Black-necked Gartersnake, Narrow-headed Gartersnake, Mexican Gartersnake, Sonora Mud Turtle

Sensitive Plant Species

The following list represents plant species that are known to occur in this habitat type:

Additional Influential Species

The following are other wildlife species, native and non-native, that can have particular influence in this habitat type. Influential species can affect SGCN and their habitats directly and indirectly, for example altering predator/prey interactions, overgrazing, outcompeting natives, creating microhabitats, and others.


American Bullfrog


Arizona Bell's Vireo, Common Black Hawk, Western Flycatcher, Gray Hawk, Green-tailed Towhee, Lucy's Warbler, Red-faced Warbler, Summer Tanager, Vermilion Flycatcher, Yellow Warbler, Yellow-breasted Chat, Zone-tailed Hawk


Black Bullhead, Blue Tilapia, Brook Trout, Brown Trout, Channel Catfish, Common Carp, Coosa Bass, Cutthroat Trout, Flathead Catfish, Green Sunfish, Largemouth Bass, Rainbow Trout, Red Shiner, Smallmouth Bass, Striped Bass, Western Mosquitofish, Yellow Bullhead


Applesnail, Asiatic Clam, New Zealand Mudsnail, Virile or Northern Crayfish, Quagga Mussel


American Beaver, Rocky Mountain Bighorn Sheep, Rocky Mountain Elk, Yuma Myotis


Huachuca Water-umbel


The following describes the primary threats facing this habitat type, adapted from Salafsky et al. (2008). First-level threats (i.e. Agriculture, Climate Change) represent broad categories while second-level threats reflect more specific stressors to the system. For detailed information on threats to this habitat type and conservation actions being taken, see Chapter 8: Threats and Conservation Actions.

1. Agriculture

1.1: Annual and perennial nontimber crops
1.3: Livestock farming and ranching
Agricultural practices adversely affect lotic systems through loss of plant cover, erosion, and dewatering caused by livestock grazing and clearing for farming. Diversions and groundwater pumping can alter habitat quality and aquatic food webs.

3. Climate Change and Severe Weather

3.1: Habitat shifting and alteration
3.2: Droughts
3.3: Temperature extremes
Climate change is leading to warmer lotic water temperatures which may surpass species’ temperature tolerances, causing local extinctions or distributions to shift towards colder water. The drying of streams can cause local extinctions or greatly reduce species distributions.

5. Disease, Pathogens, and Parasites

5: Disease, Pathogens, and Parasites
Diseases, pathogens, and parasites can spread through a variety of human-mediated mechanisms, natural processes, and movement of native and non-native fauna and can severely alter aquatic communities. Introduction of these harmful elements can also slow or end species reintroduction efforts.

7. Human Intrusions and Disturbance

7.1: Recreational activities
Recreational activities, such as illegal OHV use, are degrading lotic habitats by altering habitat, damaging instream and riparian vegetation, causing erosion in upland areas. These alterations can negatively-affect aquatic species abundance and distributions.

8. Invasive and Other Problematic Species

8.1: Invasive non-native species
Invasive and problematic species such as non-native fish, amphibians (bullfrogs), and crustaceans (crayfish), can compete with or prey upon native fauna. Invasive aquatic plants can completely cover lotic habitats. Invasive riparian area plant species, especially tamarisk and Russian olive, alter flow patterns, reduce habitat diversity, and increase shading of aquatic habitats, thereby changing food availability for native species.

9. Natural System Modifications

9.1: Fire and fire suppression
9.2: Dams and water management
Wildfire and other modifications to natural systems are resulting in silt and ash runoff, erosion that leads to increased sedimentation, and reduced water quality in lotic systems. Dams and water management activities change lotic systems to lentic systems and alter or completely dry downstream lotic systems.

10. Pollution

10.2: Industrial and military effluents
10.3: Agricultural and forestry effluents
Pollution is a mostly localized stressor to lotic systems. Effluent from mines, agriculture, and urban areas can transport a variety of pollutants that can severely degrade lotic communities.

Conservation Actions

The following describes specific conservation actions that can be taken to reduce or eliminate threats to this habitat type, adapted from Salafsky et al. (2008). Level 1 conservation actions (i.e. Land and Water Protection) represent broad categories of potential actions, while the Level 2 conservation actions (i.e. Resource and habitat protection) are more specific.

1. Land and Water Protection

1.1: Site/area protection
  • Acquire land and water rights and pursue conservation agreements and easements in and around COAs and other priority areas. (Threats 1.1, 1.3, 3.1, 9.1)

2. Land and Water Management

2.2: Invasive/problematic species control
2.3: Habitat and natural process restoration
  • Remove non-native, undesirable, and/or invasive wildlife and plant species. Monitor the success of removal efforts. (Threats 5, 8.1)
  • Install fish passage barriers to prevent upstream movement of non-native fishes into reaches with native aquatic species management emphasis. (Threat 8.1)
  • Improve, restore, or maintain high-quality aquatic habitat to support SCGN aquatic species. Develop and maintain refuge habitats. (Threats 1.3, 3.1, 9.1)

3. Species Management

3.1: Management of specific species of concern
3.2: Species recovery
3.3: Species reintroduction
  • Develop and implement projects for repatriation of wildlife species populations that are currently unsustainable or extirpated, or to improve genetic resilience throughout their historical range (including refuge populations). (Threats 1.3, 3.1, 5, 7.1, 8.1, 9.1, 9.2)
  • Establish and maintain hatchery or other captive populations and provide progeny to meet conservation needs. (Threats 1.3, 3.1, 5, 7.1, 8.1, 9.1, 9.2)
  • Rescue (salvage) native aquatic wildlife at risk from imminent threats and return salvaged wildlife when conditions are appropriate. (Threats 3.1, 3.2, 3.3, 5, 9.1)

6. Livelihood, Economic and Other Incentives

6.4: Conservation payments and programs
  • Engage landowners and partners to participate in Safe Harbor Agreements, Habitat Conservation Plans, Candidate Conservation Agreements (CCA), and Candidate Conservation Agreements with Assurances (CCAA). (Threats 1.1, 1.3, 3.1, 9.1)

4. Education and Awareness

4.3: Awareness and communication
  • Make presentations at scientific conferences, training workshops, and other professional meetings, field trips, wildlife fairs, media events, educational presentations, workshops, and public events, to increase awareness of effects of threats to aquatic and riparian wildlife species and habitats with an emphasis on how the threats can be reduced. (Threats 1.1, 1.3, 3.1, 5, 7.1, 8.1, 9.1)
  • Expand wildlife viewing programs to improve associated infrastructure (signs, platforms, etc.) and to reach larger and more diverse audiences. (Threats 4.3, 7.1)

7. External Capacity Building

7.2: Alliance and partnership development
  • Collaborate with partners across different geographies (e.g., statewide, regional, national and international) to develop and implement management plans, conservation agreements, recovery actions, research, management recommendations, and to determine the effectiveness of specific management efforts. (Threats 1.2, 3.1, 9.1)

Conservation in the Context of Climate Change

The following describes some of the conservation strategies that may mitigate the effects of a changing climate for this habitat type. Strategies have been adapted from guidelines by the Association of Fish and Wildlife Agencies (AFWA 2009).

  • Establish new wild and/or captive populations of climate vulnerable SGCN.

  • Conserve a variety of habitats that support healthy populations of fish and wildlife as climate changes.

  • Conduct research targeting species and habitat types likely to be vulnerable to climate change impacts.

Other Conservation Actions

The following describe other routine or on-going conservation actions AZGFD regularly performs in this habitat type:

  • Manage recreational activities and OHV use of riparian and aquatic habitat to minimize negative impacts to habitat and associated species.
  • Conduct surveys and monitor populations of SGCN as specified in work plans and job statements.
  • Identify the suitability of aquatic and riparian habitats for potential reintroduction or release.
  • Collect specimens or samples for taxonomic analysis, genetics, research, and/or disease testing.
  • Test novel husbandry techniques, new technology, and/or life history research on native aquatic wildlife to improve survival, growth, production, health, condition, transportation, release and post-release performance of captive progeny.
  • Fund or work with partners to conduct conservation-related aquatic species research.
  • Engage in water management public processes, such as certificated water rights and severe and transfer review and protest processes. Collaborate with partners on instream flow studies and support partner applications for instream flow water rights through sharing of species occurrence data and science.

Conservation Opportunity Areas (COAs)

The following list are terrestrial COAs where conservation efforts would benefit wildlife and their habitats. For specific aquatic COAs, refer to the COA map.

Potential Partnerships

The following is a list of the organizations and agencies that AZGFD regularly partners with on conservation efforts in this habitat type:

Important Conservation Resources

The following are relevant conservation agreements, plans, and other documents or particular interest regarding wildlife in this habitat type: