This research aimed to use the cause-and-effect diagram (model) as a method to describe the 15 main factors (for example, awareness, knowledge and motivation of farmers, farmers income, institutional and financial support, condition of the natural environment, healthiness of the population, etc.) leading to soil acidification, their impact on soil health and ecosystem functions, and how soil liming serves as a remedial measure. The cause-and-effect model was developed based on questionnaire studies as a part of the project ‘Opportunities and Barriers to the Use of Soil Liming for Improving the Economic Efficiency of Agricultural Production and Reducing Eutrophication of Surface Waters’ in 2022–2023. The results showed that the effects of soil acidification and liming as well as their interrelationships are multifaceted and affect agricultural production economics, agricultural land and crop prices, environmental health and biodiversity, as well as soil productivity and food security. The causes of this situation can be attributed to social, technological–logistical–technical, and economic factors. To change the existing situation, it is necessary to take effective steps to motivate farmers to lime their soils. The most effective would be (1) offering training courses for farmers to discuss the benefits that a farmer can achieve by maintaining optimum soil pH levels while growing a specific crop species; (2) implementing liming payment programs that will be more attractive and motivating from the farmers’ perspective; and (3) linking agri-environmental payments to the necessity of systematic testing of soil pH levels and maintaining optimal pH levels under specific crops species.