The methods of geospatial data processing are being continually innovated, and universities that are focused on educating experts in Environmental Science should reflect this reality with an elaborate and purpose-built modernization of the education process, education content, as well as learning conditions. Geographic Information Systems (GIS) have the dominant role in geospatial data processing. GIS education of students in Environmental Science (ES) in master´s degree can be divided into two main approaches - to teach about GIS and to teach with GIS. Approach "to teach with GIS" is mainly focused on teaching of Landscape Spatial Analysis with use of concrete GIS analytical tools. Students use the tools for solving of concrete problems. They work with real data and methods. The spatial analysis learned can help to manage conflicts of interest within the country, and to assess the impact of human activity on the environment. On the other hand students learn about GIS via tools and methods in concrete GIS software. To achieve higher efficiency in teaching Landscape Spatial Analysis we have created a model of GIS education based on the idea of inquiry-based learning (IBL). In an effort to get closer to the approach used for real problematic task solving, it is essential to include several interconnected systems into the education. While the Global Positioning System (GPS) Web Map Service (WMS) and Database management systems (DBMS) present the work with geospatial data similarly as GIS, Learning Management System (LMS) represents a valuable information source for students as well as an instrument for communication between teacher and students and among the students themselves during work on student projects. The proposed model can offer support of student´s motivation to learn, increased efficiency of education process and improvement preparation of students for their profession.