Many river ecosystems in the boreal zone have faced remarkable changes due to intensive human activities, including land-use changes in the catchments and channelization. Recently, restoration efforts have increased, hoping to restore a more natural hydromorphology. We studied the community structure of benthic macroinvertebrates (zoobenthos) in seven rivers in Eastern Finland, using samples that covered pre- and post-restoration periods, to examine how environmental metrics relate to the zoobenthos community structure, and the fatty acid (FA) composition and content of Ephemeroptera, Plecoptera, and Trichoptera nymphs and larvae. We also analyzed the FA composition and content of land-locked salmon (Salmo salar m. sebago) in three of the rivers and brown trout (Salmo trutta) in two of the rivers. Zoobenthos communities differed significantly among most of the rivers: 24% of the differences between the zoobenthos communities were driven by water quality parameters related to the loading of terrestrial organic matter (water color, pH, and iron concentration). Temporal changes in zoobenthos communities could not be fully attributed to restorations. The FA composition of zoobenthos was mostly explained by phylogenetic origin (47%). However, especially mayfly Heptagenia sulphurea (Ephemeroptera: Heptageniidae) had variable FA composition and content among the rivers suggesting an environmental quality indicator role for this species. FA composition and content of salmonids were mostly size-dependent (24%), but river identity also influenced their FA composition (22%). Our results indicate that water quality affects the availability of essential FAs for consumers by altering the zoobenthos community structure and their FA composition and content.