The multi-faceted aspects of natural resource governance underscore the complex nature of the subject. The intricacies associated with the skewed power relations between those who allocate these resources (land, in this case) and those who access and use them vis à vis environmental conservation make the subject a daunting one. Based on preliminary field observations and farmers’ opinions on soil health conditions in the Okavango Delta, the paper assesses the nutrient status of selected farmers’ fields and how the smallholders and government respond to this peculiar ecological environment. It specifically analyses small farmers’ perceptions on the political ecology of soil management in the area. We used a multi-stage sampling procedure to sample 228 smallholder farmers. The smallholders were interviewed using interview schedules. Key informant interviews were used to collect qualitative data from farmers as well. Thirty-three (33) composite soil samples were collected from 30 farmers’ plots in three farming communities (Makalamabedi, Nokaneng and Mohembo). Laboratory analysis shows that most soils in the wetland and its dryland surroundings are generally acidic, low in essential nutients as well as in cation-exchange-capacity (CEC). However, the results of a one-way analysis of variance (ANOVA) conducted shows significant differences in soil nutrient levels in different locations within the Delta. While farming remains an important livelihood of rural communities, policies on natural resource governance particularly along the river channels delimit local farmers’ ability to engage in meaningful soil fertility management. The low CEC of the soils is an indication that holistic cultural practices, which are beyond mere chemical fertilizations are critical and more desirable for improved soil health and sustainable rural livelihoods in the Delta.