<p>Tropical high-mountain lakes are low-temperature oligotrophic ecosystems with biological communities adapted to extreme conditions. Ecological information of these communities constitutes an important baseline, especially, facing climate change and anthropogenic activity. Hence, this study’s objective was identifying environmental variables that control spatial/temporal distribution of littoral macroinvertebrate communities in quasi-pristine lakes of Ecuador. Hydro-morphological, water quality and micro-habitat variables were monitored and macroinvertebrates sampled in 202 lakes. Further, 24 environmental variables were monitored and macroinvertebrates sampled, monthly, in 10 lakes. Twenty-two community metrics per lake were calculated. Partial Redundancy Analysis and Generalised Linear Model revealed that ecosystems response of macroinvertebrate communities to environmental variables is complex, spatially and temporally. Altitude was associated, negatively, with some richness community metrics (Total, Non-insect, Insect, Trichoptera, Odonata-Coleoptera-Heteroptera) and, positively, with the relative abundance (RA) of some taxa (<i>Andesiops</i>, <i>Anomalocosmoecus</i>, <i>Limnophora</i>). The RA of several taxa (Ostracoda, <i>Metrichia</i>, <i>Palpomyia</i>, <i>Aeshna</i> and <i>Dixa</i>) increased in larger lakes with alkaline pH (above 8.2); and in smaller lakes with higher ammonium concentrations (above 30&#xa0;μEq&#xa0;l⁻¹) (<i>Liodessus</i>, <i>Dixella</i>, <i>Rhinoaeshna</i>). Monthly macroinvertebrate community variation was not detected. However, considering three climatic phases, non-insect richness, sample RA, and the RA of <i>Helobdella</i>, and of Ephemeroptera, Plecoptera and Trichoptera, differed.</p>