# River-Wide Habitat Availability for Fish Habitat Guilds: Implications for In-Stream Flow Protection
## 1 Introduction  
The heterogeneity of habitat in a river is supported in part by variability in river discharge [1; 2]. Rivers are naturally dynamic with discharge patterns influenced by seasonal precipitation, temperature, and ground-water connections [3]. Additionally, rivers can exhibit multiple discharge patterns along their lengths [4]. The variability in river discharge can influence the spatial and temporal availability of aquatic habitat [5; 6]. For instance, increases in river discharge can enable connectivity to side-channels or floodplains whereby increasing the amount of habitat available for fishes to carry out multiple life-requisites [1]. Periods of decreased river discharge, however, can reduce the distribution of habitat types (e.g., riffle complexes and side-channels) through dewatering and may necessitate movement by fishes to refuge areas or result in declines in abundance and distribution [7]. Variability in river discharge, thus, facilitates heterogeneous habitat conditions that can influence fish species presence and abundance and subsequently fish community structure and dynamics [8; 9]. River discharge and habitat availability relationships have traditionally been evaluated at spatial scales that limit river-wide inference [6]. Evaluating habitat availability (i.e., percent of channel area) at a river-wide scale andunder different river discharges may provide the measureable unit required for the maintenance or establishment of in-stream discharges within the natural variability of the river system. Establishing relationships between river discharge and fish habitat availability at a river-wide scale necessitates habitat data that is representative of the fish community [10]. Fish species are not evenly distributed along the length of a river [11] and, thus, individual species' habitat data may not be available for a given river reach. The use of fish habitat guilds--where groups of fish species possess similar habitat needs--may enable assessment of river-wide habitat availability as the relative proportion of fish habitat guilds present can indicate changes in habitat availability [11]. Additionally, guild structure can be transferrable to different areas including river systems and potentially river reaches with dissimilar species [10]. The use of fish habitat guilds may also afford greater inclusion of discharge variability inherent to the river system. For instance, fish habitat guilds represent the integration of several species-habitat responses and provide a more ecosystem-based perspective compared to single-species habitat assessments [12; 13]. This study assessed habitat availability at different river discharges for fish habitat guilds along the Niobrara River, a large braided river system in the Great Plains, USA. Relationships between river discharge and habitat availability at river-wide scales has yet to be done in braided river systems despite the vulnerability of these systems to systemic human alteration including fragmentation and water withdrawals. Braided river systems in arid to semi-arid climates are particularly vulnerable as increased human demand for water resources and changing precipitation patterns associated with climate change exacerbate pressure on limited water supplies [14]. The objectives of this study were to: (1) Quantify habitat availability at three river discharge levels for fish habitat guilds across the length of the Niobrara River, (2) determine the suitability of aquatic habitats for each fish habitat guild, and (3) develop spatially and temporally explicit river discharge guides based on long-term river discharge data. We used the MesoHABSIM modeling framework to assess habitat availability [15]. The MesoHABSIM approach allows regional-scale assessments by modifying the data acquisition technique and analytical approach of similar models (e.g., PHABSIM) through the collection of species and habitat information at the meso-habitat scale rather than at the micro-habitat scale [15; 16].