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Along six transects in each of six lakes across the Western Balkans, we collected data for three groups of littoral biological water quality indicators: epilithic diatoms, macrophytes, and benthic invertebrates. We assessed the relationships between them and three environmental pressures: nutrient load (eutrophication), hydro-morphological alteration of the shoreline, and water level variation, separating the effect of individual lakes and continuous explanatory variables. Lake water total phosphorus concentration (TP) showed substantial variation but was not related to any of the tested biological indicators, nor to any of the tested pressures. We suggest that this may be due to feedback processes such as P removal in the lake littoral zone. Instead, we found that a gradient in surrounding land-use towards increasing urbanization, and a land-use-based estimate of P run-off, served as a better descriptor of eutrophication. Overall, eutrophication and water level fluctuation were most important for explaining variation in the assessed indicators, whereas shoreline hydro-morphological alteration was less important. Diatom indicators were most responsive to all three pressures, whereas macrophyte biomass and species number responded only to water level fluctuation. The Trophic Diatom Index for Lakes (TDIL) was negatively related to urbanization and wave exposure. This indicates that it is a suitable indicator for pressures related to urbanization, although a confounding effect of wave exposure is possible. Invertebrate abundance responded strongly to eutrophication, but the indicator based on taxonomic composition (Average Score Per Taxon) did not. Our results suggest that our metrics can be applied in Western Balkan lakes, despite the high number of endemic species present in some of these lakes. We argue that local water management should focus on abating the causes of eutrophication and water level fluctuation, whilst preserving sufficient lengths of undeveloped shoreline to ensure good water quality in the long run., Competing Interests: Declaration of competing interest We have no conflicts of interest., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)