Quantifying connectivity between functional fish habitats: A novel energy-based approach assessing multiple pathways

• Development of a habitat connectivity metric based on fish energetic swimming costs. • Novel algorithm simulates multiple paths between habitats in a 2D flow field. • Microscale quantification of grayling post-emergence rearing habitat connectivity. Fluvial ecosystems exhibit spatial heterogeneity and temporal variability, forming dynamic mosaics of interconnected habitat patches essential for fish life cycles. Access to distinct functional habitat units is crucial for survival and development across different life stages. Despite its importance, habitat connectivity modeling, particularly at the microhabitat scale, has rarely been applied in riverine research. To address this gap, we introduce Pathways , a Python-based algorithm that maps potential movement paths between patches within 2D depth-averaged hydrodynamic flow fields. Habitat Suitability Modeling is used to identify habitats of interest, while pathway feasibility is assessed by intersecting flow fields with fatigue curves that account for swimming performance. In this approach the energetic cost of each path is quantified as the time-integrated swimming power required to traverse the fluid velocity field. Habitat connectivity is assessed using the Habitat Connectivity Index ( HCI ), calculated by dividing the Weighted Usable Area of each accessible target patch by the median path energy cost of all modeled paths from a starting patch. This approach was tested on a riffle–pool reach of the Gail River, Austria, focusing on grayling larvae ( Thymallus thymallus ). Results revealed significant variations in habitat connectivity across spawning site locations and flow conditions. Mean HCI values ranged from 69.8 m²mJ⁻¹ under low-flow conditions to 3.4 m²mJ⁻¹ at mean high flow, highlighting the influence of discharge on habitat accessibility. This study provides a microhabitat-level quantification of grayling post-emergence habitat connectivity and introduces a novel framework for assessing fish dispersal and habitat accessibility.