This study provides the first decadally resolved chironomid and organic geochemistry record of the Irish Neolithic from a small lake adjacent to the Carrowkeel-Keshcorran complex in County Sligo, Ireland. Chironomid (non-biting midge fly) sub-fossils and lake sediment geochemistry (¹³C, ¹⁵N and C:N) from the Templevanny Lough core were used to assess the timing and magnitude of within-lake responses to Neolithic farming activity. When compared with decadally resolved pollen and macroscopic charcoal records from the same core, the limnological data show a direct influence of prehistoric farming on a freshwater lake system through nutrient loading and lake eutrophication. Elevated nutrient levels, suggesting a more productive lake system, and a subsequent turnover in the chironomid community indicate a period of intensive farming activity from c. 3790–3620 BC in the early Neolithic. This was followed by a decline in farming with short periods of small-scale human activity, exemplified through nutrient loading and short-lived increases in eutrophic chironomid taxa during the middle to late Neolithic. A return of farming activity can be seen in all proxy data in the late Neolithic (c. 2720–2480 BC). The chironomid community composition typically lagged land-use change by c. 10–20 years and exhibited predictable and proportional responses to agricultural activity. The timing and magnitude of limnological changes show that land-use, rather than climate, is the main control on chironomids at Templevanny Lough, thus showing the potential prominence of the anthropogenic signal during the Neolithic.