The aim of the study was to analyse the evolution of the prevalence of HAV and HEV in the population of eastern Spain by analysing the viruses excreted in urban sewage. Raw urban sewage samples were collected and analysed during several years using RT-PCR techniques and sequencing analysis. Two limiting regions were analysed, one of them having implemented HAV vaccination programs. Acute symptomatic HEV cases were also examined. Results were compared with those from previous studies in the area using identical methodology. The percentage of positive HAV samples in urban sewage fell from 57.4% to 3.1% in 5–10 years in the two studied areas in Spain. Around 30% of the urban sewage samples were positive for HEV in the absence of agricultural sources of contamination. HEV RNA was also detected in four clinical cases of acute hepatitis. The dramatic reduction in the presence of HAV in raw urban sewage observed in eastern Spain could be most likely related to the general improvement in sanitation. However, these improvements would not have an equivalent effect on the circulation of HEV and this observation could be explained by the presence of animal reservoirs for HEV, which act as external sources of infections.