Floodplains and associated lakes are important components of the biogeochemistry, ecology, and hydrology of the Amazon basin. Amazon floodplains contain thousands of lakes and associated wetlands linked to each other and to the many rivers of the immense basin. These floodplain lakes modify the passage of flood waves (Richey et al. 1989a), increase nutrient retention and recycling (Melack and Fisher 1990), and influence the chemistry of the rivers (Devol et al. 1995). The mosaic of flooded forests, open water, and floating macrophytes in the central Amazon floodplain makes a significant contribution of methane to the troposphere (Bartlett et al. 1988, Devol et al. 1990). The fishery potential of the large river systems is closely tied to the area of floodplain and the magnitude and duration of inundation (Welcomme 1979, Bayley and Petrere 1989). The majority of fishes harvested in the Amazon basin obtain nutrition in flooded forests (Goulding 1980) or from organic matter derived from floodplain algae (Araujo-Lima et al. 1986, Forsberg et al. 1993). Much progress has been made during the last fifty years toward understanding the lakes of the Amazon floodplain. Still, the vast size of the Amazon basin poses challenges to limnologists working in the region. Recent research has been enhanced by the maintenance of functional floating laboratories in several areas, use of modern ships capable of regional surveys and equipped for hydrographic studies, and applications of remote sensing. Our objective in this chapter is to examine the role of lakes in the hydrology of the floodplain and in the biogeochemistry of carbon, nitrogen, and phosphorous within the central Amazon basin. Particular emphasis is placed on how inundation patterns interplay with carbon balance and nutrient limitation. By combining numerous measurements of primary productivity with recent results from studies using isotopes of carbon, we will examine the contribution of the major plant groups to aquatic foodwebs, and offer a new paradigm for the processing of organic carbon on the Amazon floodplain. The interplay between the Amazon River and local catchments as sources of nutrients to the floodplain indicates the potential sensitivity of the lakes to basin-wide and local disturbances.