While many studies provide microscale relationships between fish and habitat characteristics, studies covering longer river reaches are scarce. Modern remote sensing techniques may enable new and effective ways of mapping and assessing mesoscale habitat characteristics. Using green LIDAR-derived bathymetry and hydraulic modelling, we tested how mesoscale depth and velocity were related to fish counts of adult European grayling (Thymallus thymallusL.) and brown trout (Salmo truttaL.) in 500 m river sections in three separate periods during the year. Using riverbank sinuosity from aerial images and a Froude number-based index from the hydraulic model as proxies for mesoscale spatial and hydraulic heterogeneity, we tested for temporal correlations with river section fish counts of adult European grayling and brown trout. Results showed that mesoscale mean depth and velocity were correlated to period fish counts of adult European grayling. Using mixed model analysis we found that riverbank sinuosity and the Froude number-based index were significantly correlated with river section occurrence of adult European grayling during spawning. The results can be used to assess how flow-induced changes and channel adjustments at the mesoscale level can influence access to and use of relevant habitats in rivers occupied by European grayling and brown trout.