Poland’s traditional, i.e., non-GIS, regionalization needed to be updated for landscape audit purposes. Its spatial accuracy appeared insufficient, which led to the verification and adjustment of the existing physical-geographical mesoregions using GIS and high-resolution spatial data. In Poland, provincial landscape audits are part of implementing the European Landscape Convention to Polish law order, which led to the renewal of interest in the natural spatial division of the country. To date, there is no unified division of the entire country into microregions, which in Poland are commonly perceived as the most appropriate natural spatial units for local-scale landscape analysis and management. Microregions are lower-rank spatial units than already existing mesoregions. Both are distinguished by a homogenous landscape defined within the specific area by common physical-geographical characteristics of the land. Nevertheless, each is recognized at different scales and levels of generality. This paper focuses on reviewing the current challenges of the physical-geographical regionalization of Poland. Their fundamentals were identified through a systematic literature review. It also presents all the problems encountered within implementing GIS in the microregionalization procedure, which was already used for the Greater Poland Voivodeship landscape audit. In general, all traditional methodologies related to the physical-geographical regionalization of Poland require the introduction of GIS solutions to meet the current expectations from the country’s contemporary natural spatial division. The landscape contrast analysis method proved to be a promising method of GIS-based regionalization. It has the potential to become a universal solution to the existing problems with a unified physical-geographical microregionalization of Poland. However, some hard-to-overcome obstacles are related to the availability, collection, and processing of all required thematic spatial data. Nonetheless, it is highly expected to develop a universal procedure of microregionalization and distinguish low-rank units for the entire country.