Nipuni's research focus is mainly on environmental fluid mechanics. She has worked on solute transport mechanisms in complex open channel flow regimes and and solute/microplastic transport across the hyporheic zone. She also works on vegetation induced wave attenuation.

In addition to that, Nipuni has previously worked on breakwater stability and has experience on transdisciplinary research in sustainability science. Nipuni is interested in interdisciplinary research that propose solutions for the environmental problems faced by the humanity.