Fine sediment is a leading cause for the decline of aquatic biodiversity globally. There is an urgent need for targeted monitoring to identify where management methods are required in order to reduce the delivery of fine sediment to aquatic environments. Existing sediment-specific biomonitoring indices and indices for general ecological health (taxonomic and trait-based) developed for use in the UK were tested in a representative set of lowland rivers in England that consisted of a gradient of fine sediment pressures (deposited and suspended, organic and inorganic). Index performance was modelled against environmental variables collected during sampling and hydrological and antecedent flow variables calculated from daily flow data. Sediment-specific indices were indicative of surface sediment deposits, whereas indices for general ecological health were more closely associated with the organic content of fine sediment. The performance of biotic indices along fine sediment gradients was predominantly dependent on hydrological variability. Functional diversity indices were poorly related to different measures of fine sediment, and further development of traits-based indices and trait databases are recommended. In summary, the results suggest that sediment-specific biomonitoring tools are suitable for evaluating fine sediment stress in UK rivers when index scores are viewed within the context of local hydrology.