Abstract Host-parasite relationships can be directly affected by host’s biological aspects and environmental factors, which influence both the survival of infective forms and the incidence of parasites. However, logistical difficulties in accessing biological samples for parasitological studies makes the Amazon Forest into a poorly known region in relation to the dynamic of parasites of wild animals. Here, using 34 red howler monkeys’ biological samples donated by local subsistence hunters from two Amazon habitat types (white-water flooded forest and upland forest) as an opportune alternative, we detected four intestinal parasite taxa infecting this species (two nematodes – Trypanoxyuris sp. and Strongyloides sp., one protozoan – Entamoeba sp. –, and one not-identified trematode, the last just found for white-water flooded forest). Trypanoxyuris was the most prevalent intestinal parasite (56.5% at flooded forest and 54.5% at upland forest). There was no difference between habitat types or individual sex regarding the prevalence for any parasite taxa. On the other hand, we found a strong influence of seasonality, with increasing prevalence of all parasite taxa as the river water level increased. In terms of egg and cyst counts, we found a difference between sexes (females > males, p = 0.002) and habitat types (upland forest > white-water flooded forest, p = 0.02), and a positive relationship with river water level (p = 0.002). Although some of these parasite taxa can be shared between humans and howlers, further investigations are necessary to study the parasites taxonomy thoroughly and to assess the potential zoonotic cross-transmission of these pathogens to local people living in the Amazon. In this study, we unveiled a seasonal effect for howler monkeys’ intestinal parasites, that also might occur in other non-human primates of the Amazon. In addition, our results on periods of high risk of intestinal parasite infection are useful to estimate future impacts of climate change on host-parasite dynamics.