Flooding in the Okavango Delta is very variable both at short and long term time scales. The variation in flooding strongly affect users of water and wetland resources, and the temporal and reversible effects of climatic variation and non-linearity of the Okavango Delta hydrological system are often confused with the effects of system change that are permanent and irreversible. Understanding of causal factors of changes in flooding in the Okavango Delta observed currently and in the past is necessary for determining future prospects and is critical for preventing unnecessary development pressure and for wise management of the world largest Ramsar site. Hydrometric data and satellite-derived inundation areas are analysed here using statistical methods (covariance analysis) to distinguish between temporal and permanent changes in various parts of the Okavango Delta. The results show that statistically significant changes in the input-response relationship occurred in the past in various parts of the Okavango Delta. Depending on the presence and direction of change in neighbouring distributaries, some of these changes are interpreted as effects of system nonlinearity, some however, as resulting from physical change in the system. The high flow regime of one of the distributaries, the Boro, observed in 1974-1981, earlier thought to result from physical change in the system was re-interpreted as an effect of system non-linearity, triggered by an exceptionally high rainfall. A physical change in the system is the likely explanation of the relative increase in flooding of one of the distributaries, the Xudum, observed recently. The results suggest that the increase in Xudum flooding took place at the expense of the Thaoge, and not, as previously thought of the Boro. Keywords: Okavango, wetlands, flood, change.