This publication presents the results of studies of the bottom sediments (sapropels) of lakes in the North Kazakhstan region. The purpose of this study is to identify the possibility of using sapropels from the lakes of the region in obtaining innovative fertilizers for organic farming. For this purpose, geoinformation technologies, field research, statistics, and chemical and chemical-analytical methods were used (automated spectrometric methods of segmented flow analysis, photocolorimetry, flame photometry, and inductively coupled plasma atomic emission spectrometry). During the first stage of this study, the bottom sediments of three lakes in the region, which were at different stages of eutrophication, were selected to study the chemical composition of the raw materials. The sapropel of Lake Penkovskoye had optimal indicators. Further, an analysis of the territory of the region for the development of agrotourism was carried out. The aim of this study is to substantiate the prospects for the use of sapropel in the production of innovative fertilizers. The natural origin of sapropels allows them to be used in the production of environmentally friendly and safe products. Reducing the use of artificially synthesized mineral fertilizers will make agriculture and the environment safe and sustainable. This will further contribute to the development of agrotourism in the region.