The Iberian Peninsula is located along the East Atlantic and Black Sea/Mediterranean flyways and is the third ranking European country as wintering quarter for wild migrating birds after Turkey and Rumania. For these reasons, Spanish wetlands are of importance in AIV surveillance, and of great interest for the study of the epidemiology of LPAIV under Mediterranean climate conditions. Nevertheless, information on prevalence of LPAIV viruses in Spain is still scarce and is restricted to two serological surveys carried out in the south of the country during 1990 and 1994 and one virological study performed recently in North East Spain. In the present study we analysed the prevalence of AIV circulating in wild birds in continental wetlands in central Spain and determined temporal, spatial and species variation. Real time RTPCR was performed on 1435 faecal samples and cloacal swabs from 54 species. An overall AIV prevalence of 2.6% was detected with a peak during November and December, when thousands of migrating wild birds arrive to Spain for wintering. Highest prevalence rates were detected in Phoenicopteriformes and Anseriformes. AIV prevalence obtained from cloacal swabs and fresh faeces did not vary significantly, which supports faecal sampling as an appropriate method for large scale LPAIV surveillance programs. Viral culture was achieved in samples obtained from two Mallards and a White stork, in which subtypes H7N9 and H11N9, respectively, were identified. Our results reflect a similar scenario in AIV epidemiology in small continental wetlands as compared to large coastal humid areas in Europe and underline the importance of including species such as flamingos and storks in surveillance programs, since their role in AIV ecology in these areas could be more important than previously considered.