According to historical sources, a watermill existed in the valley of the Trojanka River on the north-western shore of Raduszyn Lake from the 15th century. Its dams lasted for centuries causing the water flow through the Raduszyn reservoir to slow down and deposit various mineral fractions in it. The aim of paper was to develop a scientific background for the sustainable management of organic matter extracted from the peat top and from deeper layers that are unsuitable for direct use, that is, decomposed peat. A SWOT (strengths, weaknesses, opportunities, threats) analysis was used to describe ways of restoration of the water reservoir alongside the characterization of organic matter and the financial condition of the studied enterprise. For the use of the studied material as a homogeneous substrate for plant cultivation, the contents of nitrogen, phosphorus, potassium, and copper were insufficient, whilst calcium was excessive. Microbiological analyses of the organic materials intended as an additive for horticultural substrates confirmed the presence of plant growth-promoting bacteria. The occurrence of such microorganisms in the substrate can limit the use of mineral fertilizers and chemical plant protection products. The results of the research can be an example for enterprises restoring or creating water reservoirs by extraction of organic matter, which is often considered as waste that generates costs and does not bring financial benefits. Such a measure can be used to improve the efficiency of water reservoir restoration enterprises and at the same time contribute to sustainable land development.