The cave site known as Matja Kuru 2 (MK2) in Timor-Leste was first occupied ∼40 kya. Of the caves investigated thus far in Timor-Leste MK2 is unique in being located proximal to a large freshwater lake, Ira Lalaro, providing the opportunity to examine changing occupation dynamics in a lakeside environment from the Late Pleistocene through to the late Holocene. We present the analysis of the Matja Kuru 2 assemblage including the stone, ochre, shell and bone artefacts, and the vertebrate and invertebrate remains. We discuss the challenges posed by cave deposits in tropical Island South East Asia which often preserve little in the way of identifiable stratigraphy. Such caves also present challenges in terms of disentangling what components of the faunal assemblage were deposited as meal refuse by humans, as opposed to by other predators or as a result of natural deaths. We suggest a method for assisting with this taphonomic conundrum.