Ancient lakes, such as lakes Ohrid and Prespa on the Balkan Peninsula, have become model systems for studying the link between geological and biotic evolution. Recently, the scientific deep-drilling project Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) was initiated to better understand the environmental, climatic, and limnological evolution of the lake. It revealed that Lake Ohrid experienced a number of environmental disturbances during its ca. 2.0 million year long history. These are comprised of disturbances that lasted over longer periods of time ("press events") such as glacial-interglacial cycles and Heinrich events, as well as sudden and short disturbances ("pulse events") like the deposition of landslides, earthquakes, and volcanic ash depositions. The latter includes one of the most severe volcanic episodes during the Late Pleistocene: the eruption of the Campanian Ignimbrite (known as Y-5 marine tephra layer) from the Campi Flegrei caldera, dated to 39.6 ± 0.1 thousand years ago. The event is recorded by the deposition of a ca. 15 cm thick tephra layer in sediment cores of lakes Ohrid (DEEP-5045-1) and Prespa (Co1204). Coincidently, this pulse event is superimposed by the Heinrich H4 event, 40.4-38.4 thousand years ago. In the current paper, diatoms were used as proxies to compare the responses of these lakes to the Y-5 (pulse) and the H4 (press) disturbances. Based on stratigraphically constrained incremental sum of squares cluster (CONISS) and unconstrained Partitioning Around Medoids (PAM) analyses, we found little evidence that diatom community compositions in either lake responded to the H4 event. However, the Y-5 influx caused clear and rapid diatom community changes. After the initial response, community compositions in Lake Ohrid and, to a lesser extent, in Lake Prespa slowly returned to their quasi pre-disturbance state. Moreover, there is no evidence for disturbance-related extinction events. The combined evidence from these findings suggests that lakes Ohrid and Prespa likely did not experience regime shifts. It is therefore concluded that both lakes show resilience to environmental disturbance. However, it seems that Lake Ohrid is more resilient than Lake Prespa, as the recovery of diatom communities is more pronounced and its estimated recovery time is only ca. 1100 years vs. ca. 4000 years in Lake Prespa. The reasons for the differential responses remain largely unknown, but differences in geology, lake age, limnology, and intrinsic parameters of the diatom proxies may play an important role.