<p>Wetlands are fragile ecosystems, usually sensitive to cross-boundary transport of matter and biologically available energy from adjacent ecosystems. In the case of the Pantanal, land use change in the adjacent highland, the damming of upstream rivers and weather fluctuations exert important influences on the ecosystem dynamics. The individual impact of these cross-boundary factors to the water availability in the Pantanal are described in the literature, but no joint assessment considering each factor is assessed yet. Thus, this paper takes advantage of the increasing availability of environmental and modelling approaches to estimate the relative contribution of weather, upstream river damming and highland land cover changes to the observed water cover reduction in the Pantanal. The results suggest that native vegetation clearing around springs and riverbeds in the adjacent highland of the Pantanal have the relatively largest contribution to surface water reduction in almost four decades, followed by pasture and cropland expansion in the highland and drier weather both in the high- and lowland. As practical conservation guidelines, taken from the model´s outcomes in consonance with the literature, three main measures are proposed in their respective order of importance: (1) recovering the vegetation around springs and river margins in the highland by solving the on farm deficit of native vegetation in permanent protection areas; (2) promoting a transition from monocultures to sustainable and diversified agroecosystems in the highland, and; (3) restricting the construction of new dams in the rivers that flow to the Pantanal.</p>