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To advance current environmental flow standards in Texas, we developed field, laboratory, and analytical methods to model recruitment dynamics of indicator species selected to cover a range of population responses to flow variation. Preliminary investigations were conducted in three central Texas river basins to evaluate the feasibility of these methods for formulating and evaluating the state's environmental flow standards. Age analysis allowed back‐calculation of dates of fish hatching, mussel recruitment, and tree germination for estimation of temporal variation in recruitment. Recruitment data were then analyzed in relation to flow regime components. Statistical models were derived for flow–recruitment relationships of Shoal Chub Macrhybopsis hyostoma, Smallmouth Buffalo Ictiobus bubalus, threeridge mussel Amblema plicata, and boxelder Acer negundo. The Shoal Chub model was used to hindcast recruitment dynamics in the Brazos River, revealing a decline in recruitment after dam construction. The Smallmouth Buffalo model revealed that strong year‐classes were positively associated with springtime pulses of long duration but negatively associated with frequent short‐duration pulses. Results for the threeridge mussel were not as easily interpreted, but for all three river basins generally showed weaker recruitment during periods with extreme low and high flows. The boxelder model revealed positive associations between recruitment and high flow components and was used to forecast the probability of germination under five simulated flow regime scenarios, thereby providing an additional means for evaluating the suitability of environmental flow standards. Assessment of how hydrology influences recruitment provides an evidence‐based method to hindcast responses to past flow regimes and forecast responses to future flow scenarios, thereby providing a basis for evaluating environmental flow standards and water management options.

The Guadalupe bass Micropterus treculiiis endemic to Texas and is threatened by introgression with introduced smallmouth bass M. dolomieuas well as habitat degradation. This study described and quantified the movements and habitat associations of Guadalupe bass to assess the factors that may influence current populations. Radio-tagged adult Guadalupe bass were tracked in the Pedernales River (n= 12) and South Llano River (n= 12) from January through August 2008. Available microhabitats were measured and modeled in terms of depth, velocity, substrate, and cover for about 1.5 km in the Pedernales River and 1.2 km in the South Llano River. Rates of movement were greatest during the reproductive season, ranging from less than 1 to 9 m/d. Instream cover (such as undercut banks and woody debris) was preferred during daylight hours throughout the study period, although the distances from cover increased from January to August. Habitat shifts from cover to open water occurred at night and from woody structures to boulders and ledges during a large flood pulse. The habitats most suitable for adult Guadalupe bass had a depth of 1.0 m and a current velocity of 0.05 m/s, and habitat selection was strongest for eddy mesohabitats with smaller substrates. By July, the Guadalupe bass in the South Llano River were associated with runs with greater current velocities, whereas those in the Pedernales River were associated with pools with greater depths, largely owing to the low flows and reduced habitat availability in the Pedernales River. Environmental factors, including the availability and suitability of instream cover, are probably the strongest influences on the distribution and abundance of Guadalupe bass.

Most state-of-the-art applications of habitat modelling rely on three-dimensional channel topography and two-dimensional hydrodynamic models that have centered on the simple extension of one-dimensional physical habitat-based concepts (i.e., extension of the Physical Habitat Modelling System - PHABSIM). However, as demonstrated in this paper, these approaches can be extended to more realistically incorporate both the physical habitat-based metrics of streamflow and behavioural decision rules that can incorporate fish community structure and dynamics. This approach evaluates the spatial suitability of physical habitat-based on the incorporation of behavioural rule sets, such as the association with escape cover type and distance, exclusion zones associated with predators or linear dominance hierarchies, and lag-time dependence of macroinvertebrate re-colonization of habitats associated with varial zones induced by peaking/load following operations of hydropower facilities. In the paper we lay the foundation between field data collection strategies for characterization of the physical domain, and modelling the hydraulic properties of flow using two- or three-dimensional hydraulic models. We then describe the use of GIS for the integration of additional factors such as substrate, cover, distance to cover and distance to water’s edge factors. We then demonstrate how GIS, in conjunction with decision based habitat algorithms, can be used with classical-based physical habitat modelling to incorporate behavioural-based rules to evaluate escape cover, exclusion zones and lag-time dependence for macroinvertebrate under variai zone induced impacts. These examples are based on results from studies in regulated river systems in which these techniques have been shown to improve the assessment of impacts/benefits associated with altered flow regimes.