The study of exogenous metabolites of algae-bacterial communities in the laboratory accumulative culture obtained from natural river water was conducted using gas chromatography-mass spectrometry. Exometabolites of the algae-bacterial community (including microalgae and cyanobacteria) in the culture medium were represented by saturated, unsaturated, and aromatic hydrocarbons, carboxylic acids, phenolic, and terpene compounds and their derivatives. Possible biological activities of the discovered exometabolites are considered. The study has demonstrated that an increase in the number of main groups of microorganisms, along with changes in the composition of algae and cyanobacteria, are responsible for the increase in the composition and concentration of metabolites in the microecosystem’s culture medium after one month of cultivation. The presence of octacosane in high concentration (0.0603 mg/L; 23.78% of the total content of low molecular weight organic compounds) by the end of exposure accumulative culture is associated with the strong development of the cyanobacterium Gloeocapsa sp. in the presence of diatom algae of the genus Navicula and green algae of the genera Chlorella and Scenedesmus. Due to the need to comprehend the ecological and biochemical mechanisms of the formation and functioning of algae-bacterial communities, as well as to predict potential paths of transformation and evolution of aquatic ecosystems, the specificity of exometabolite complexes of algae and microorganisms, as well as their allelopathic and other biochemical interactions in freshwater ecosystems, requires further serious study.