| Few studies were based on the temporal variation in birds of South-East Benin. In order to study the temporal variation of birds population in Aguégués, some ornithological survey were carried out monthly from August 2017 to July 2018 by the method of punctual abundance indexes enabled the counting of 14191 individuals gathered into 268 species, 55 families and 18 orders. In Aguégués, the highest mean specific richness and birds’ abundance were observed respectively in BDS with 45 ± 22.37 species and 561 ± 240.81 individuals though the lowest values were recorded in BRS with respectively 23 ± 12.5 species and 324 ± 355.43 individuals. The picks of mean specific richness and abundance reached in BDS corresponded to the period of migratory birds coming to the South-East Benin wetland. A high positive correlation and highly significant to the 5% threshold (cor = 0.87; t = 15.178; df = 11; p-value = 1.007e-08) were noticed between the monthly fluctuation of mean number and the mean specific richness by the student test for pair series. The highest mean indexes of Shannon-Weaver (2.99±0.60) and the Pielou mean equitability (0.88±0.04) were recorded respectively in BDS and BRS. The lowest respectively 2.40±0.58 and 0.77±0.09 were calculated in BRS and SRS. The mixed linear model generalized showed the monthly variations of ecological indexes among stations are significant to the 5% threshold except plantations, Lake Nokoué and Porto-Novo lagoon. Besides, monthly variations are not due to the random effect of months (R² marginal < R² conditional).