Toxic cyanobacterial blooms are a well-known problem in eutrophic water bodies, but cyanobacterial toxicity in ambient springs is unexplored. Therefore, we studied the toxin content and effects of two extracts obtained from epilithic and benthic microbial mats containing different algae and filamentous cyanobacteria, Phormidium breve and Oscillatoria limosa, respectively, on fresh biomass, number of roots, and pigment content in duckweed Spirodela polyrhiza and on survivorship of Daphnia magna (Cladocera). Mat samples, used to prepare extracts for bioassays, were collected in the anthropogenically transformed limnocrenic Górecko spring, located (50°31′08″ N and 22°57′10″ E) in the Roztocze region (Eastern Poland). It drains an abundant aquifer built with Cretaceous sediments. Neither anatoxin-a (ANTX) nor microcystins (MCs) were detected in the extracts using HPLC techniques; however, negative effects of the extracts on tested organisms were observed. The Phormidium extract contained concentrations of cyanobacterial metabolites a few times higher than the Oscillatoria extract. In general, both extracts affected plants in a dose-dependent manner; however, the Oscillatoria extract influenced pigment production without a clear trend. The highest concentrations of Phormidium extract (p < 0.05) significantly decreased the number of roots and the content of chlorophylls and carotenoids in S. polyrhiza. The Oscillatoria extract caused a statistically significant (p < 0.05) decrease in biomass and number of roots; however, it generally positively influenced the production of pigments. The extract containing O. limosa metabolites was more toxic to D. magna than the extract containing higher amounts of metabolites of P. breve. Cyanobacteria inhabiting temperate springs may negatively affect hydrobionts by producing secondary metabolites other than ANTX and MCs; however, the contribution of algae cannot be excluded. Extensive research on cyanobacteria in springs, their metabolites, and their effects on living organisms should be conducted.