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Background Zoonotic pathogens respond to changes in host range and/or pathogen, vector and host ecology. Environmental changes (biodiversity, habitat changes, variability in climate), even at a local level, lead to variability in environmental pathogen dynamics and can facilitate their transmission from natural reservoirs to new susceptible hosts. Whilst the environmental dynamics of aquatic bacteria are directly linked to seasonal changes of their habitat they also rely on the ecological processes underpining their transmission. However data allowing the comparison of these ecological processes are lacking. Here we compared the environmental dynamics of generalist and vector-borne aquatic bacterial pathogens in the same unit of time and space, and across rural and urban habitats in French Guiana (South America). Principal findings Using Leptospira sp. and Mycobacterium ulcerans we performed an environmental survey that allowed the detection of both pathogens in urban vs. rural areas, and during rainy vs. dry weather conditions. All samples were subjected to qPCR amplifications of LipL32 (Leptospira sp.) and IS2404 and KR (M. ulcerans) genetic markers. We found (i) a greater presence of M. ulcerans in rural areas compared with Leptospira sp., (ii) that modified urban environments were more favourable to the establishment of both pathogens, (iii) that Leptospira sp. presence was enhanced during the rainy season and M. ulcerans during the dry period, and (iv) differences in the spatial distribution of both bacteria across urban sites, probably due to the mode of dissemination of each pathogen in the environment. Conclusions We propose that in French Guiana simplified and modified urban ecosystems might favour leptospirosis and Buruli ulcer emergence and transmission. Moreover, disease risk was also constrained by seasonality. We suggest that the prevention of aquatic bacterial disease emergence in impoverished urban areas of developing countries would benefit from seasonal diseases targeted surveys, which would maximise limited budgets from cash-strapped health agencies., Author summary Many emerging pathogens are zoonotic and transmit from their abiotic reservoir to wild animals, domesticated animals and humans. It is now well known that environmental changes lead to variability in their dynamics in the environment and contribute to changes in the infectious risk. Many aquatic bacteria are responsable for major public health concerns, and more importantly in developing countries where access to drinking-water and sanitation is often limited. Whilst their environmental dynamics are directly linked to seasonal changes of their habitat, they also rely on the ecological processes underpining their transmission, i.e. directly transmitted vs. vector-borne. However, few studies have compared such environmental dynamics despite the fact that it would help to better characterise the infectious risk in the environment, as well as to better monitor the emergence of infectious diseases. Our aim was to provide data on the prevalence of generalist vs. vector-borne aquatic bacterial pathogens in the environment that would further allow the comparison of their environmental dynamics in the same unit of time and space, and across rural and urban habitats. We showed that urbanization and seasonality are two important factors underlying Buruli ulcer and leptospirosis disease emergence in French Guiana (South America), and propose that the mode of transmission of such environmental pathogens might have a detrimental role in disseminating the infectious agent in the environment.