Lacustrine sediment sequences were obtained from Lagunas Verde and Gemelas Este, two small lakes located east of the southern Patagonian Ice Field and close to the village of El Chalten, in Argentinian Patagonia. Four tephra layers were identified in each of the short sediment sequences and characterised using individual glass-shard tephra chemistry to determine provenance. Bulk sediment geochemistry and diatom assemblages were analysed to understand the impact of the tephra deposits on the lake ecosystems. Age-depth models for the cores were established by 137Cs and 210Pb dating. Tephra deposits in Laguna Gemelas Este were dated to AD 1986–1998, 1943–1968, 1927–1955, and 1849–1892, and the tephra deposits in Laguna Verde were dated to AD 1940–1970, 1888–1934, 1871–1920, and 1536–1669, the latter interval determined by extrapolation. All tephras had similar geochemical composition and originated from volcanoes in the northern Austral Volcanic Zone. Tephra units were attributed to known historical eruptions and all but one, most likely, were from Lautaro Volcano (49°01′S; 73°33′W). The age of the youngest tephra (AD 1986–1998) from Laguna Gemelas Este points to Viedma Volcano (49°22′S; 73°19′W) as a possible source. Volcanic eruptions had a larger impact on Laguna Verde than on Laguna Gemelas Este, as expressed by changes in δ15N values and diatom communities during tephra deposition. These shifts are explained by perturbations of the nitrogen cycle in the lake, associated with shifts in lacustrine primary production. Primary producers may have been affected by increased water turbidity caused by the ash fall, and consequently, used less nitrogen. Diatom assemblages in Laguna Verde showed marked reductions in numbers of planktonic/tychoplanktonic taxa, in favour of epiphytic/benthic diatom taxa, when tephra was deposited. This contrasts with Laguna Gemelas Este, in which epiphytic/benthic diatom species were generally more abundant and decreases in abundances of planktonic/tychoplanktonic taxa were not as strongly linked to tephra layers as in Laguna Verde. At Laguna Gemelas Este, flatter relief, greater fetch and/or drier climate may have contributed to generally less ecosystem variability, resulting in seemingly less environmental response to volcanic eruptions than in Laguna Verde.