Data collection for poverty assessments in Africa is time consuming, expensive and can be subject to numerous constraints. In this paper we present a procedure to collect data from poor households involved in small-scale inland fisheries as well as agricultural activities. A sampling scheme has been developed that captures the heterogeneity in ecological conditions and the seasonality of livelihood options. Sampling includes a three point panel survey of 300 households. The respondents belong to four different ethnic groups randomly chosen from three strata, each representing a different ecological zone. In the first part of the paper some background information is given on the objectives of the research, the study site and survey design, which were guiding the data collection process. The second part of the paper discusses the typical constraints that are hampering empirical work in Sub-Saharan Africa, and shows how different challenges have been resolved. These lessons could guide researchers in designing appropriate socio-economic surveys in comparable settings.