Research has been conducted on the development of an innovative organomineral fertilizer based on local lake resources as a stimulator of germination and growth of crops, as one of the factors in achieving the goal of environmental sustainability. The results obtained are based on the environmental friendliness of the technology, increasing yields, and obtaining environmentally friendly products. This, in turn, will not only save mineral resources but also make it possible to use the resources from the bottom sediments of local lakes, and their rational extraction will contribute to the sustainable development and restoration of lake ecosystems. This article highlights the results of laboratory and field studies on the use of sapropel extract at the stage of pre-sowing seed treatment obtained by extraction of bottom sediments from lakes in Northern Kazakhstan. Solutions of aqueous alcohol extract of sapropel extract with concentrations of 0.4, 0.8, 1.2, 1.6, 2.0 g/L and table beet seeds (Beta vulgaris L.) of Bordo 237 variety were used as objects of research. Statistical analysis of laboratory experience data, based on the determination of germination energy and seed germination, allowed us to identify the optimal concentration of sapropel working solution for pre–sowing seed treatment—1.6 g/L. The index of germination energy and germination of seeds during pretreatment with sapropel extract of this concentration was 40% and 50%, respectively. This contributed to an increase in germination energy by almost 2 times and in seed germination by more than 40%. Pre-sowing treatment of seeds with sapropel extract at a concentration of 1.6 g/L in a field experiment contributed to the improvement of biometric indicators of beet fruits, such as diameter, length, and weight. The results of the data on fetal weight of the experimental variant compared with the control were 27% higher, and they were 26% and 32% higher compared with other experimental variants. In the experimental group, the highest yield index was also established, which is 2.15 times, or 53%, higher than the control, which emphasizes the effectiveness of pre-sowing seed treatment with the resulting sapropel suspension. A patent of the Republic of Kazakhstan was issued for the method we developed for obtaining a sapropel product for pre-sowing treatment of seeds: “A method for obtaining a sapropel product for pre-sowing treatment of vegetable seeds”. The research presented in the article confirms its effectiveness. The use of this product in pre-sowing seed treatment reduces the number of agrotechnological operations and costs, which makes this method more efficient and economically beneficial for the agricultural industry. Thus, the principle of food security will be implemented, contributing to the preservation of sustainable development and having a positive impact on the health of the population.