Physicochemical properties of expanded vermiculite-phlogopite products from Kovdor (Murmansk region, Russia) used for 15 years as a hydroponics substratum were studied. The four investigated samples were as follows: natural vermiculite, initial expanded (roasted at 700 °C) vermiculite, spent expanded vermiculite and spent vermiculite roasted again at the same temperature. Data on the bulk density, field capacity, hygroscopicity, and expansion coefficients showed that the degradation of the substratum was accompanied by mechanical destruction, reduction of water absorption by half, and transformation of mineral phases. The structural transformation of expanded vermiculite was studied using X-ray diffraction (XRD), thermogravimetric analysis (TG), and differential scanning calorimetry (DSC), coupled with a mass spectrometric analysis of the released gases. Under conditions with a sufficient supply of plants with potassium of nutrient solution, a change in the mineral composition occurred: a decrease in the content of vermiculite and an increase in phlogopite. The formation of organomineral complexes on the surface of the vermiculite was detected. There was no noticeable change in the chemical composition of the expanded vermiculite during its use in hydroponics. In essence, the levels of potentially toxic elements (Mn, V, Ni, Cr, Co, Cu, Zn) met environmental regulations, and the levels of major elements (Mg, Ca, K, Fe, Mn) corresponded to those found in natural vermiculite. The chemical composition and structure of spent vermiculite allows its use as an ameliorant to improve soil, water, and air regimens.