The El Niño–Southern Oscillation (ENSO) is a globally important factor in today's climate dynamics. Annually laminated oil shales from the maar lake of Messel (Germany) provide high-resolution sedimentological and paleoenvironmental data of a time interval of ∼600 k.y. during the Eocene greenhouse phase. Individual laminae consist of a light spring and summer algal layer (Tetraedron minimum layer) and a dark winter layer composed of terrigenous background sediment. Four sections were selected from the core of the Messel 2001 well in order to count varves and to measure total varve thickness and the thickess of light and dark laminae. Spectral analyses were done in order to detect possible cyclic fluctuations in varve thickness. Fluctuations are significant in the quasi-biennial (2.1–2.5 yr) and low-frequency band (2.8–3.5 yr, 4.9–5.6 yr), thus showing that algal growth as well as the background sedimentation were controlled by ENSO effects at least over a time interval of 600 k.y. This confirms the existence of a previously postulated robust Eocene ENSO. Significant peaks within a quasi-decadal (10–11 yr), interdecadal (17–26 yr), and multidecadal band (∼52 yr, ∼82 yr) show either the enduring influence of more or less cyclic instabilities or the influence of solar cycles.