a b s t r a c tWe present an assessment system for determining the ecological status (eutrophication and land use pressures) and non-indigenous macroinvertebrate species (NIMS) specific deviation from naturalness of Lithuanian lakes, using semi-quantitative sampling of littoral macroinvertebrates. This system includes two integrated indices, the multimetric Lithuanian Lake Macroinvertebrate Index (LLMI) and the Fauna Autochthony Index (FAI). The LLMI, developed for the assessment of ecological status, averages four metrics: the conventional Average Score Per Taxon (ASPT) and the first Hill's number (H 1 ), as well as the newly validated number of Coleoptera, Ephemeroptera and Plecoptera taxa (#CEP) and the proportion of Coleoptera, Odonata and Plecoptera individuals (COP). Furthermore, the metrics of biocontamination were transformed into the WFD-compliant FAI for the NIMS-specific naturalness evaluation.The LLMI had significant correlations with total phosphorus, total nitrogen, chlorophyll a, biochemical oxygen demand, water transparency, the morphoindex and the combined trophomorphoindex. Relationships between the LLMI or its core metrics and biocontamination were not found; thus the LLMI and the FAI are not interdependent and have the advantage of separately accounting for pressures requiring different management techniques. Variation of the LLMI and the FAI did not differ between stony/pebbly and vegetated littoral mesohabitats suggesting that any of the mesohabitats or a multihabitat sampling technique can be suitable for a reliable evaluation of lake status.Aquatic beetles revealed themselves as good indicators of the trophic status, while caddisflies and conventional macroinvertebrate metrics ETO and EPT proved unworkable. The ineffectiveness of the latter metrics may be due to the relatively low trophic level in most of the studied lakes which resulted in an increment of caddisfly metrics with an increase of nutrient loads, as well as due to the susceptibility of caddisflies to the invasive species, the zebra mussel Dreissena polymorpha and amphipod Pontogammarus robustoides.