A complex Holocene system in the central Iberian Range (NE Spain) has been reconstructed on the basis of sediments recovered from cores and in situ observations. Small alluvial fans graded into a wide shallow lacustrine area (Añavieja Lake) that connected downstream with a carbonate fluvial system with associated vegetated zones. The fluvial system was mainly characterized by the development of tufa barriers (especially during the first part of the Holocene) that separated pools or small lakes. Oncolites, detrital tufas, calcarenites and marls were deposited in these pools. Adjacent vegetated areas were covered by macrophytes and were episodically reached by detrital tufa supplies indicating high flood stages. High sedimentary rates existed in both the fluvial (including the pools) and vegetated areas suggesting that, despite the common erosion of tufas, a clear aggradating evolution existed. By contrast, very low sedimentary rates were registered in the Añavieja Lake. All the environments, but especially the vegetated areas, registered the climate evolution during the Holocene. Although the onset of the Holocene was characterized by wide climate variability, warm and humid conditions dominated during the first part and drier conditions during the second part. A water level recovery seems to have been existed during the last millennium. This is a good example of the potential of continental systems other than lakes to be useful for palaeoenvironmental and palaeoclimatic studies.