Aims: Population numbers and trends of overwintering waterbirds were updated for Santoña Marshes Nature Reserve (N Iberian Peninsula). Methods: Census data of December and January, carried out between 2001/2002 and 2005/2006, were analysed to obtain overwintering population numbers, and thus update the status of Santoña Marshes for migratory waterbirds. To examine trends, these data were compared with the ones obtained in the same months between 1997/1998 and 2000/2001. The potential influence of temperature in the abundance of waterbirds was also analysed. Results and Conclusions: Santona Marshes supported an average of 19,848 overwintering waterbirds during the analysed period. The total number showed a positive rate of population change between the two analysed periods, this being 46 %. The temperature registered in Santona was correlated with the abundance of some species, but not with the total number of waterbirds. This coastal wetland represents an Area of National Importance during winter for 18 waterbird species. It is also an Area of International Importance for the Icelandic population of black-tailed godwit Limosa limosa islandica. There were significant trends for ten species at Santona Marshes, eight increasing and two decreasing. The increasing trends in the populations of the species under study, along with the improvement in the ecological conditions of the feeding habitat, could explain, in general terms, the population increases of waterbirds registered in Santona Marshes in the last nine years.