The diatom stratigraphy of a 23-m sediment core from Lake Tilo, a maar lake in the Ethiopian Rift Valley, provides a 10,000-yr record of lake salinity and trophic status. Until 5500 14C yr B.P., the phytoplankton was dominated by Aulacoseira granulata, with only minor changes in the abundance of other diatoms; the lake was over 50 m deep, eutrophic, and oligosaline. At 5500 yr B.P., geothermal groundwater inflow, inferred from calcite and silica deposition rates, declined abruptly, and the lake became more oligotrophic, as indicated by a rapid rise in Cyclotella stelligera. About 4500 yr B.P., lake salinity began to increase, reaching approximately its present state ca. 2500 yr B.P., but with a temporary reversal to lower salinity at 4000–3500 yr B.P. The record shows no evidence of salinity increases equivalent to early Holocene low stands of the larger river-fed Rift Valley lakes, probably because of high rates of geothermal groundwater influx. It responded to reduced rainfall at 4500 yr B.P., when levels of the larger lakes also fell, because geothermal groundwater flux had diminished 1000 year earlier, independently of climate. Because geothermal groundwaters can form a significant proportion of a crater lake's hydrological budget and dominate its salinity budget, these results show that variable geothermal groundwater flux can override lake hydrochemical response to climate change. Palaeoclimatic interpretation of palaeosalinity proxies from the sediments of volcanic crater lakes should be approached with caution.