This paper summarises the results of on-going research on the valley floor by a multidisciplinary team of archaeologists and specialists in soils, pollen and phytoliths. The research project is designed to chart the history of human occupation of this complex and frequently flooded area during the Holocene and the interaction between this environment and the human population. In the mountains surrounding much of the upper and central Cauca valley there is a gap in our knowledge of human occupation of a thousand years and more with the most recent dates for preceramic sites in the third millennium B.C.; furthermore these later sites appear to be far less numerous than those known from earlier in the Holocene. This "archaeological silence" comes to an end about 700 B.C., by which time the area was inhabited by established farmers with sophisticated pottery. The period of silence is precisely when we would expect to find evidence for early Formative activity in the area, including an intensification of horticulture. Project results, so far, include evidence for local climatic fluctuations with wetter and drier periods, tentative evidence (burning) for human disturbance of the environment from very early in the Holocene (late IXth millennium B.C.) and firm paleobotanical evidence from one or probably two sites for cultivation (maize and arrowroot) associated with burning or other forms of disturbance of the vegetation within the period of "archaeological silence". Although no artefacts from this period have been found so far, a considerable number of sites were located from the late Formative period (Ilama and its daughter culture, Yotoco), testifying to a much more intensive occupation of the valley floor and its floodlands at this time than had been documented previously.