The spectral decomposition of time series obtained from ancient rock records can be used to study the similarity between the dynamics of present-day and past climate systems. A high-resolution periodicity analysis of luminance and lamina thickness of lacustrine stromatolites in the Ebro Basin (northeast of Iberian Peninsula) reveals a significant signal of interannual and decadal climatic variability in the Miocene. This is one out of very few works that presents the use of spectral analysis to estimate the potential of stromatolite lamination as multiple-scale recorders of climate parameters. The effects of precipitation and evaporation variations on stromatolite lamination have been detected at three orders of cyclicity based on textural and high-resolution stable-isotope analyses (C and O) obtained in prior studies. These analyses also revealed that the light and dark simple lamina couplets are identified with annual cycles (third-order isotopic cycles). In the present study, the spectral analysis results obtained through different paths in five stromatolite specimens reveal significant periods in the power spectrum at around 2.5, 3.7, 5, 7, 10, and 22 years. These cycles can be correlated with the typical oscillation bands of different climate-related agents. The 2.5-year period corresponds to the Quasi Biennial Oscillation (QBO), or to the biennial component of the El Niño-Southern Oscillation (ENSO), or to the North Atlantic Oscillation (NAO). The 3 to 5 and 5 to 7-year bands can be linked to ENSO or NAO variability (second-order isotopic cycles). The 8 to 11-year bands fit the 11-year Schwabe (first-order isotopic cycles) and 22 to 23-year fit the 22-year Hale sunspot cycles. Thus, the stromatolite growth was controlled by ENSO, NAO, and solar activity cycles. The close relationship between these climate-related agents makes it difficult to specify the dominant agent controlling the stromatolite growth. Nevertheless, the significant periods obtained from this study, within interannual (2.5, 3.7, 5, 7 years), decadal (10, 22 years), and even multidecadal bands (37–42 years), support the existence, and concurrence, of ENSO and NAO precursors during the early and middle Miocene.