The Antillean manatee Trichechus manatus manatus is a cryptic mammal that inhabits, among other areas, murky rivers and estuaries of Central and South America. The difficulty in detecting and counting manatees is an obstacle to monitoring their population status, as traditional count sampling is unsuitable. We conducted a quantitative analysis of the distribution and abundance of the manatee across its known range in the rivers and estuaries of French Guiana, based on data from a range-wide line transect visual survey combined with a side-scan sonar survey, identification of feeding sites, and silent observations at fixed points. A total effective effort of 248 hours and 1,129 km of boat survey was completed. We used two relative abundance indices: the combined encounter rate, which combines encounters per km from either visual or side-scan sonar surveys, and the global detection index, which is defined as the sum of all evidence per unit time. Manatees were detected in all nine study units. Niche modelling was used to analyse the space selection by manatees, and helped to detect differential use of habitats according to the season. The model predicted that coastal areas are used more extensively during the dry season. In the absence of better techniques to detect wild manatees in complex habitats this monitoring protocol may be relevant and replicable in hydrological systems where manatee detectability is constrained by biogeographical characteristics.