This study explored the utility and performance of chironomid (Diptera: Chironomidae) autecology in the investigation of prehistoric farming impacts on freshwater lake systems. Chironomid subfossils, lake sediment geochemistry (delta C-13, delta N-15 and C:N), pollen and macroscopic charcoal analyses were used in a comparative limnological assessment of three archaeologically rich study sites in northwest Ireland. At all three study sites, pastoral farming and its associated nutrient inputs, as represented by non-arboreal pollen indicative of grassland/pasture (NAPp) and lake sediment geochemistry, are concomitant with increases in eutrophic chironomid taxa. Redundancy analysis (RDA) and partial RDAs established that delta N-15 and NAPp were controlling factors of chironomid community compositional change during the Neolithic (4000-2500 BC) and Bronze Age (2500-600 BC). Bronze Age farming had a considerably greater impact on the lake systems than Neolithic farming, as indicated by a higher proportion of eutrophic taxa and increases in delta N-15, C:N and delta C-13 values, consistent with increased erosion and agricultural inputs. Findings emphasise the importance of identifying the natural, pre-impacted state of a lake system to determine the extent of agricultural impact accurately. The timing and magnitude of change show that Neolithic and Bronze Age farming exhibited a strong control over chironomid communities at all three sites.