1. Eutrophication has been shown to increase production of nutritionally low-quality cyanobacteria and decrease the long-chain polyunsaturated fatty acid (PUFA) content of seston. Contrarily, lake browning inhibits cyanobacteria contribution in seston and favours poorly grazable mixotrophic algal species. These environmental changes have probable impacts on the diet and long-chain PUFA content of primary consumers. However, herbivorous zooplankton may preferentially retain PUFAs through diet selection for optimal growth and reproduction, but such selective feeding is challenging to document in nature owing to the difficulties in quantifying zooplankton diet.2. Here, we sampled seston and herbivorous cladocerans (Daphnia sp. and Bosmina sp.) from lakes (n = 23) in Finland along eutrophication (total phosphorous) and browning gradients (dissolved organic carbon [DOC]). We analysed the fatty acid content of seston (mg FA/g POC [particular organic content]) and cladocerans (mg FA/g C), and estimated available and consumed diet biomass percentages with quantitative fatty acid signature analysis. Cladoceran diet preference was evaluated as the difference between consumed and available food sources, to understand if they preferentially retain high nutritional quality diet.3. Generally, lake chemistry and morphometry poorly explained seston and cladoceran long-chain PUFA contents. However, multiple linear models for shorter chain PUFAs (linoleic acid [LA] and alpha-linolenic acid [ALA]) performed better in explaining variation in the LA and ALA content of seston (20% and 11%) and cladocerans (36% and 46%, respectively). The factors most strongly and positively associated with the LA and ALA content of seston and cladocerans were phosphorus and DOC concentrations, respectively. 4. Seston and cladoceran PUFA contents were clearly uncorrelated. In most of the sampled lakes, high-quality diet (i.e., diatoms and cryptomonads) was preferred by cladocerans and low-quality diet (cyanobacteria) was avoided. Lake chemistry poorly explained cladoceran diet preference, but high-quality preference was positively associated with lake average depth.