Nepal is a country rich in water resources and biodiversity. Many river basins across Nepal also have high potential for hydropower generation as well as irrigated agriculture which will enhance economic development in the country. However, careful management of water resources is required to protect freshwater ecosystems. This can be advanced by building capacity in the country to undertake integrated, multidisciplinary science. Environmental monitoring that highlights the response of ecological assets such as birds, fish, vegetation, invertebrates, crocodiles, and the Ganga dolphin to hydrological alteration is therefore important to inform water extraction timing and limits. A literature review indicated that little research had been undertaken to monitor river-flow ecology relationships and many key knowledge gaps exist. A small, integrated, seasonal study was undertaken at the Koshi Tappu Wildlife Reserve in southeast Nepal to model approaches to freshwater ecosystem monitoring that could assist in identification of likely indicators of environmental change as well as preliminary thresholds to change. The study focussed on measuring river flow and chemistry changes in relation to macrophyte, bird and invertebrate presence and biomass, whilst upskilling Nepali students and supervisors to undertake integrated field research linking hydrological and ecological changes in aquatic systems. Links were also made to livelihood impacts such as extreme floods which removed access to vital protein sources such as snails and denuded river substrates of reeds that provide income sources through basketry.