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In some coffee-growing municipalities in the departments of Caldas and Risaralda, in the Central Zone of Colombia, coffee crops are at risk due to extreme climatic variations. In order to evaluate the relationship between the changes in production systems and the variations in biophysical elements, information from all coffee farms located in the municipalities of Santuario and Balboa (Risaralda) and Salamina (Caldas) was collected in the years 2006, 2009, 2012 and 2015. Statistics regarding production, age, density, and varieties, among others, were determined. Data about temperature and rain retrieved from the climatic networks of the IDEAM and the Red Cafetera were analyzed. The values of water excess and deficit as well as soil moisture index were obtained from the water balance calculation. The changes between years and by physiological stages of the crop were evaluated. The results show that Salamina and Santuario decreased their coffee area between 2009 and 2015, while Balboa increased it. Threat factors were related to water excess (Santuario and Salamina) and deficit (Balboa). In all the municipalities, the greatest vulnerability occurs in areas below 1,300 m.a.s.l., under El Niño conditions, 2015, related to temperature increase and annual water supply decrease. The biophysical condition (climate and soil) was not associated with the dynamics of change, in area and coffee crops, in the studied municipalities.