Guinea-Bissau is host to the westernmost subpopulation of the common hippopotamus Hippopotamus amphibius, which is one of only two known populations inhabiting coastal waters. The presence of hippopotamuses causes conflict with rice farmers as a result of crop damage and the absence of effective measures to protect crops. To develop an effective method for protecting rice fields, we studied the patterns of access to flooded and rain-fed rice fields by hippopotamuses and assessed the effect of the installation of electric fences. Hippopotamuses were detected in 54% of the flooded fields (n = 100) and in 31.9% of the rain-fed fields (n = 91). They were detected more frequently in fields on offshore islands than on the mainland, in unfenced than in fenced fields, and in fields closer to running water. Hippopotamuses entered fenced flooded fields less frequently than unfenced, and were detected most frequently at the end of the rainy season and the start of the dry season, and in the period of vegetative stem growth. Electric fences were an effective deterrent and facilitated increased rice production. The maintenance and cost of the electric fencing were acceptable to farmers, and therefore the use of such fencing is recommended to resolve the conflict between hippopotamuses and farmers in Guinea-Bissau and in other areas with similar conditions.