Addressing soil salinity in irrigated drylands is tightly linked with water and land management decisions thus requiring interdisciplinary engagement. The salinity mapping approaches in Central Asia are undertaken through field sampling and laboratory analysis, which is a time consuming process. As a consequence, salinity maps are not available on time to estimate water requirements to cope with varying levels of soil salinity. Reducing the time lag between assessment and delivery of such maps would enable authorities to determine in advance appropriate water volumes for leaching the salts before and during the growing season. Research initiated in Uzbekistan context explored transdisciplinary and participatory approach to innovation development with local stakeholders. As one of the innovations, an electromagnetic induction meter (EM), a tool for rapid salinity assessment, was chosen and jointly with local salinity mapping related institutions tested, validated, and local capacities for its use developed. This paper redraws this process of innovation-focused stakeholder interaction and transdisciplinary research and discusses it with reference to ongoing debates on participatory and/or transdisciplinary innovation research. The existence of strong path dependencies within implementation oriented organizations could be observed, meaning that the innovation demands many changes to the existing system. Furthermore, the encountered challenges of participatory, transdisciplinary research in the hierarchically shaped setting of post-soviet Uzbekistan are illustrated in selected qualitative field notes and assessed. For improved joint learning and research in a transdisciplinary team, feedback cycles of mutual learning and critical reflection of how to theoretically and practically work in a transdisciplinary manner turned out to be crucial and not to be underestimated.