Saproxylic insects of the infraorders Bibionomorpha and Tipulomorpha (Diptera) are ecologically important components of forest ecosystems, associated with dead wood and contributing to nutrient cycling and food webs. Despite their diversity, the influence of climatic variables on saproxylic nematoceran communities remains poorly understood. This study examined the effects of precipitation, air temperature, and relative humidity on the abundance, species richness, and diversity of saproxylic nematoceran flies in three Lithuanian nature reserves from 2016 to 2020. In total, 793 specimens representing 10 families were collected using trunk-emergence traps. Statistical models showed that precipitation was significantly positively associated with species richness, total abundance, and Shannon’s diversity, whereas temperature and humidity were excluded as non-significant predictors. These results highlight precipitation as a key environmental driver shaping saproxylic fly assemblages and suggest potential sensitivity of these communities to reduced moisture availability under future climate change scenarios.