The increasing global population and the simultaneous growing attention to natural, sustainable, and healthier products are driving the food industry towards research on alternative food sources. In this scenario, microalgae are gaining worldwide attention as “functional feedstocks” for foods, feeds, supplements, and nutraceutical formulations, being a source of high-value metabolites including polyphenols and other antioxidant compounds. In this work, eleven microalgal strains from freshwater environments were evaluated for their nutraceutical properties, focusing on photosynthetic pigments, total polyphenols, and flavonoid content, as well as in vitro antioxidant activities. Data helped to select those strains showing the most promising features for simultaneous massive growth and bioactive compound production. Results highlighted that the microalgae have variable values for both biochemical parameters and antioxidant activities, mainly depending on the solvents and applied treatment rather than on the isolation sources or the phylogenetic attribution. According to our results, the putative best candidates for massive cultivation under laboratory conditions for the simultaneous extraction of different molecules with nutraceutical potential are strains F1 (Scenedesmaceae), F3 (Chlamydomonas debariana), R1 (Chlorella sorokiniana), and C2 (Chlorella-like).