A survey of chironomid subfossil remains was carried out in Lough Muckno, a lake system located in northeast Ireland. The dataset provides new insights into chironomid ecology and subfossil taphonomy in the Irish Ecoregion. A significant degree of homogeneity in subfossil assemblages and presence of efficient offshore redeposition mechanisms was evident. The potential role of the thermocline and river discharge in determining subfossil assemblage composition was also explored. Redundancy analysis indicated that sample (spatial) location and water depth are governing and intertwined controls on chironomid assemblage composition. Profundal habitats at a sensible distance from the littoral best integrated basin-wide remains representing suitable locations for paleoecological reconstructions based on a single-core approach. However, assemblages in deep mid-lake habitats characterized by advanced diagenesis and low head capsule counts were deemed unsuitable for paleoecological applications. The results highlight the importance of accounting for both lake depth and distance metrics in the design of paleolimnological investigations in systems with a complex basin morphology.