Floodplain lakes are biodiversity hotspots whose ecological functioning is strongly controlled by hydrological connectivity and flow variability. This study investigates the relationships between hydraulic conditions and benthic macroinvertebrate habitat suitability in Jama Roma, a representative floodplain lake of the near-natural Bug River system in eastern Poland. The lake is characterised by a contrafluent–confluent exchange regime, in which the direction and magnitude of river–lake connectivity vary dynamically with flood stage. A two-dimensional ecohydraulic model (Iber v3.3.1) was used to simulate spatial and temporal patterns of water depth and flow velocity during a real flood event. Habitat suitability was assessed using field-derived habitat preference curves based on macroinvertebrate sampling data, supported by biodiversity metrics and statistical analyses of relationships between hydraulic variables and macroinvertebrate occurrence. The results demonstrated that the highest habitat suitability and macroinvertebrate abundance occurred under moderate hydraulic conditions, particularly at depths of 0.5–1.0 m and velocities below 0.15 m/s. Spatial and temporal changes in hydrological connectivity strongly influenced the distribution and persistence of suitable habitats, with low-velocity littoral and central lake zones functioning as key ecological refugia during floodplain inundation. The study advances ecohydrological assessment of floodplain lakes by integrating dynamic hydrodynamic modelling with field-based biological preferences in a spatially explicit framework. Beyond site-specific findings, the results provide environmentally relevant reference conditions for near-natural floodplain systems and demonstrate a transferable approach for evaluating flow–habitat interactions in river–floodplain landscapes under changing hydrological regimes.