Central Asian countries have experienced a transition from a centralized state-managed economy to a decentralized market-oriented one, and gained valuable experience in designing institutions involving common-pool resource (CPR) management. Top-down policy interventions have affected natural resource usage practices and had environmental, social and economic consequences. On the other hand, in a bottom-up transformation process, many informal practices for using local resources and many forms of cooperation have emerged and become institutionalized, adapting to the changing socio-economic context. This paper demonstrates an empirical application of the Institutions of Sustainability (IoS) framework, analyzing these emerged institutions, and governance structures in pasture and irrigation management. It studies how the physical nature-related transactions are institutionalized through the operationalization of a discriminative alignment principle. The research results show that actors’ interdependencies caused by the attributes of nature-related transactions play a decisive role in institutional development in CPR management in Central Asia. The authors argue that differences in the properties of physical nature-related transactions in pasture and irrigation water use can be linked and explained through differences in the key characteristics of governance structures.