Lake Menjer is one of the crater lakes located in the highland of Central Java, Indonesia, which has received multiple stressors from anthropogenic activities. Benthic macroinvertebrates as a key indicator for water quality were little known there. Thus, this present research aimed to identify benthic macroinvertebrate structures and to understand the response of this community to water quality in Lake Menjer. Samplings were conducted twice, one week each in August and October 2019 at five sites. Sampling in August represented the condition of the dry season, while in October represented the rainy season. Some groups were identified into the family and others into the genus level. Water quality variables were measured directly on the site, including water clarity, pH, dissolved oxygen (DO), conductivity, total dissolved solids (TDS), and oxidation-reduction potential (ORP). Meanwhile, the level of total nitrate (TN), total phosphate (TP), nitrite, and chlorophyll-a were analyzed separately. A total of 4312 benthic macroinvertebrates composed of eleven taxa belonging to eight families were recorded, namely Chironomidae (22.85%), Tubificidae (73.50%), Lumbricullidae (0.68%), Thiariidae (0.21%), Planorbidae (0.45%), Lymnaeidae (0.21%), Unionidae (0.92%), and Corbiculidae (1.13%). The number of taxa varied between 1 to 3 in each station. Mollusk was the best-represented group with five families. Meanwhile, Tubificidae was shown as the predominant family in abundance both in August (3879 ind/m2) and October (2008 ind/m2). Shannon-Wiener index ranged nearly similar between the two seasons, 0.17 to 0.91 in August and 0.0 to 0.91 in October. ANOSIM CAP6 result illustrated that there was an insignificant difference in benthic macroinvertebrates abundance (P below 0.05) among sampling sites in Lake Menjer. This community was mostly homogenous. Bray-Curtis analysis using MVSP shows similarities in the taxa compositions between the sites. The analysis between water quality and macroinvertebrates which was performed by Canonical Correspondence Analysis shows that nine taxa tended to correlate with the level of TN, DO, and conductivity. Meanwhile, the other two taxa had a relationship with water clarity, temperature, level of TP, nitrite, and chlorophyll-a.