The Nile crocodile,Crocodylus niloticus, is found throughout sub-Saharan Africa, including Namibia, Botswana and Angola. The species was transferred from CITES Appendix I to Appendix II in 2004, although it is recognized as peripherally endangered in Namibia due to diminishing habitat availability primarily from human encroachment. In 2013, a species management plan was approved in Namibia to assess the management of the Namibian Nile crocodile populations. During 2012, an aerial survey was conducted to provide an estimate of Nile crocodile population numbers. A recently developed N-mixture model for estimation of abundance and spatial variation was used. Detection probability correlated to animal size and environmental covariates. Our data also suggest that small crocodiles are easier to detect during the spring. The abundance for different size classes was influenced by river complexity (vegetation, depth, channels) and the distribution of human settlements. An estimated 806 individuals were counted along the 352 km Namibian portion of the Kunene River system with a conservative estimate of 562 crocodiles regardless of size. The parameter estimates generated by the analysis suggested that the class-structured model can produce reliable estimates of total abundance and of local abundance for this section in the Kunene River system.