Recognizing how stream fish communities-and their habitats-differ across space and time relative to their position in stream networks (i.e., main-stem versus tributary habitats) is increasingly important for the conservation of imperiled native fish communities in altered river networks such as those in the Colorado River basin. We studied the patterns (community composition) and processes (movements) that shape species occurrences and distributions in two tributaries of the San Juan River, Utah and New Mexico, between 2012 and 2014. Our results show that distance from the San Juan River was a strong driver of tributary fish community structure, whether through declines in species richness (Chaco Wash) or species turnover (McElmo Creek), and that these patterns coincided with habitat gradients (i.e., depth, substrate, and width). Occurrences of passive integrated transponder (PIT)-tagged fish at a stationary antenna in McElmo Creek just upstream of its confluence with the San Juan River varied by species but generally were associated with spring spawning migrations (Flannelmouth Sucker Catostomus latipinnis, Razorback Sucker Xyrauchen texanus), exploratory movements (Colorado Pikeminnow Ptychocheilus lucius), and monsoon flooding (Channel Catfish Ictalurus punctatus, Razorback Sucker). Occurrences of PIT-tagged fish in Chaco Wash were dominated by endangered Razorback Suckers and Colorado Pikeminnows, suggesting that this habitat supplies useful habitat, forage, or both. Given the common occurrences of native fishes in these tributaries, incorporating these habitats into basinwide management actions seems necessary to fully understand the spatiotemporal dynamics of native and nonnative fish communities.

Quantifying fish movements in river networks helps identify critical habitat needs and how they change with environmental conditions. Some of the challenges in tracking fish movements can be overcome with the use of passive integrated transponder (PIT) tagging and antennas. We used PIT technology to test predictions of movement behaviour for four fish species at a mainstem-tributary confluence zone in an arid-land river system. Specifically, we focused on the McElmo Creek tributary confluence with the San Juan River in southwestern Utah, USA. We quantified variation in species occurrences at this confluence zone from May 2012 to December 2015 relative to temporal and environmental conditions. We considered occurrences among species relative to tagging origins (tributary versus mainstem), season and time of day. Generally, fishes tagged in the focal tributary were more likely to be detected compared to fish tagged in the mainstem river or other tributaries. Additionally, adults were most likely to be detected across multiple years compared to subadults. Based on a Random Forests model, the best performing environmental variables for predicting seasonal detections included mainstem discharge during run-off season (razorback sucker Xyrauchen texanus), tributary discharge during monsoon season (Colorado pikeminnow Ptychocheilus lucius) and mainstem water temperature (flannelmouth sucker Catostomus latipinnis and channel catfish Ictalurus punctatus). The variable responses by endemic and introduced fishes indicate tributary habitats provide several key functions within a fish community including spawning, rearing, foraging and refuge. K E Y W O R D SCatostomus latipinnis, confluence, edge effects, movement behaviour, PIT tag, Xyrauchen texanus | INTRODUCTIONQuantifying movements of freshwater fish has been difficult due to logistical challenges of tagging and recapturing highly mobile individuals (Albanese, Angermeier, & Dorai-Raj, 2004;Gowan & Fausch, 1996;Rodriguez, 2002). Accordingly, conceptual frameworks such as the restricted movement paradigm (Gerking, 1959), long distance dispersal (Rodriguez, 2010) and confluence exchange hypothesis (Thornbrugh & Gido, 2010) that predict patterns of movement in riverine systems need testing with empirical studies. Despite the challenges studying riverine movement, advances in tagging methods now allow for freshwater fish populations within diverse communities to be studied at greater spatial and more continuous temporal scales (Cooke et al., 2013;Gowan, Young, Fausch, & Riley, 1994;Young, 2011).Sampling continuously allows increased detectability of diverse movement behaviours within and among species compared to discrete sampling events (Fausch, Torgerson, Baxter, & Li, 2002;Schlosser & Angermeier, 1995;Wiens, 2002). Intensive temporal sampling can be optimised by selecting detection sites that maximise our ability to capture the diverse inter-and intraspecific movement behaviours across time. types (Bottcher, Walsworth, Thiede, Budy, & Speas, 2013;Kiffney, Green, H...

Human transformation of aquatic systems and the introduction of nonnative species increasingly threaten the persistence of imperiled freshwater fishes. In response, large‐scale mechanical removal of nonnative fishes has been implemented throughout parts of the Colorado River basin to aid recovery of endangered fishes, but the effects of these efforts can be difficult to quantify. Fisheries population models for predicting outcomes of harvest regulations have been widely used to prevent overfishing of commercial and game stocks. Here, we used population models to investigate size‐specific removal efforts needed to overfish a nonnative population of Channel Catfish Ictalurus punctatus and thereby aid recovery of endangered fishes in the San Juan River, New Mexico and Utah. The minimum size of fish that were efficiently captured with electrofishing gear was 280 mm TL, and annual removal rates increased with fish size, ranging from 0.10 for 200‐mm fish to 0.44 for 600‐mm fish. Model results suggested that removal rates should be increased from 0.14 to a range of 0.21–0.34 to cause growth overfishing and should be increased to a range of 0.26–0.29 to cause recruitment overfishing at a minimum electrofishing size limit of 280 mm TL. However, model results indicated that overall population abundance and biomass are being substantially reduced compared to an unmanaged population. In concordance, long‐term monitoring data from 1991 to 2015 demonstrated a decrease in Channel Catfish TL and mass as well as an increase in catch rate variability since removal efforts intensified in 2006. Overall, current rates of removal will probably not achieve collapse of the nonnative Channel Catfish population in the San Juan River, but the reduction in size structure indicates that the population has responded to these efforts.

Unforeseen interactions of dams and declining water availability have formed new obstacles to recovering endemic and endangered big‐river fishes. During a recent trend of drying climate and declining reservoir water levels in the Southwestern United States, a large waterfall has formed on two separate occasions (1989–1995 and 2001–present) in the transition zone between the San Juan River and Lake Powell reservoir because of deposited sediments. Since recovery plans for two large‐bodied endangered fish species, razorback sucker (Xyrauchen texanus) and Colorado pikeminnow (Ptychocheilus lucius), include annual stockings in the San Juan River, this waterfall potentially blocks upstream movement of individuals that moved downstream from the river into the reservoir. To quantify the temporal variation in abundance of endangered fishes aggregating downstream of the waterfall and determine population demographics, we remotely monitored and sampled in spring 2015, 2016, and 2017 when these fish were thought to move upstream to spawn. Additionally, we used an open population model applied to tagged fish detected in 2017 to estimate population sizes. Colorado pikeminnow were so infrequently encountered (<30 individuals) that population estimates were not performed. Razorback sucker captures from sampling (335), and detections from remote monitoring (943) showed high abundance across all 3 years. The razorback sucker population estimate for 2017 alone was 755 individuals and, relative to recent population estimates ranging from ~2,000 to ~4,000 individuals, suggests that a substantial population exists seasonally downstream of this barrier. Barriers to fish movement in rivers above reservoirs are not unique; thus, the formation of this waterfall exemplifies how water development and hydrology can interact to cause unforeseen changes to a riverscape.

Reservoirs and associated river fragments are novel ecosystems not experienced by fishes in their evolutionary history, yet they are now commonplace across the globe. Understanding how fishes use these novel habitats is vital to conservation efforts in contemporary riverscapes. Movement patterns of the endangered razorback sucker (Xyrauchen texanus) synthesized from tagging efforts in the upper Colorado River basin, USA, illustrate the applications of tagging technology and data sharing by multiple agencies to better understand the spatial ecology of large river fishes. Tagging studies between 2014 and 2018 in Lake Powell and its two main tributary rivers, the Colorado (unfragmented) and San Juan (waterfall‐fragmented), were used to quantify movement of razorback sucker within this river–reservoir habitat complex. In addition, facilitated translocations of fish upstream of a waterfall barrier in the San Juan River were assessed in 2016–2017. Extensive movement of fish occurred within and across river and reservoir habitats. Of 722 fish captured in the Colorado River arm of Lake Powell, 36% of re‐encounters occurred upstream in the Colorado or Green rivers, or fish dispersed through the reservoir and were detected in the San Juan River arm. Fourteen fish moved more than 600 km. In the San Juan arm of the reservoir, 29% and 20% of fish in 2017 and 2018, respectively, had moved ~30–40 km upstream below the waterfall in the San Juan River within a year. In 2016–2017, 303 fish were translocated upstream of the waterfall into the San Juan River, but 80% were re‐encountered downstream of the waterfall within a year. Long‐distance movements by razorback sucker were common within and among rivers and reservoirs illustrating how large river fish, in general, might maintain population connectivity in highly altered ecosystems.