We monitored egg clutch numbers of a population of the endemic Italian agile frog Rana latastei in a Site of Community Interest in northern Italy (SCI IT 209000) during 1997–2017 with the aim of assessing the long-term variation in its abundance. We walked along the banks of canals and small ponds (n = 22) 1–3 times per week between early February and mid-April each year to detect egg clutches. The relationships between the start of the breeding season, yearly egg mass counts, rate of yearly change in the number of recorded egg masses and 15 climatic and environmental variables were assessed by multiple regression. The first deposition of eggs occurred progressively later in the year throughout the study period and mean air temperature during the breeding season decreased over this period. Agile frogs showed high deposition site-fidelity. Despite large variations in the number of egg clutches detected from year to year, the population size remained stable in the long term. Peaks in the number of egg clutches occurred 2 years after the dredging of canals, carried out every 4–6 years to improve water availability, starting in 2004 as part of a LIFE Nature Project. This was the only predictor of the number of egg clutches deposited, suggesting that periodical management is needed to support the agile frog population. Our results reinforce the need for multi-year monitoring to determine both the long-term success of habitat restoration projects and the status of residual populations.