Zooplankton fatty-fatty acid data from Swedish lakes along a temperature (summer temperatures 6.8–15.9°C), water color (< 0.005–0.51 Abs420), and eutrophication ( mean TP < 1.0–42.3 μg P L−1) gradient encompassing 2002–2010 and 2020–2021 periods (n=100, N=32 lakes). The dataset is divided into two sheets: one with the fatty acid data ("Zooplankton fatty acid data"), and another with the mean lake data ("Lake data"). A third sheet ("metadata") explains the metadata and the abbreviations used in the other two sheets.