Engraulicypris sardella is an endemic and economically important cyprinid species in Lake Nyasa/Malawi which has recently been infected by the tapeworm Ligula intestinalis. This parasite is known to induce severe pathological and behavioural effects on other cyprinids, including castration, followed by a collapse of infected populations. As a first step to understanding the dynamics between this parasite and E. sardella, we studied the spatial and temporal variation in prevalence over a period of 1 year. Overall prevalence was about 15%, but we observed a consistently higher prevalence in the littoral compared to the pelagic zone. Fish in the upper water levels showed the highest prevalence, with a marked decline with increasing water depth down to 150 m. The proportion of infected fish varied over time, with a significantly higher prevalence in the rainy season. In a huge lake like the Nyasa, with a surface area of 29,000 km2 and a maximum depth of 785 m, the transmission success of the parasite appears to show large variations in time and space. We suggest that these conditions could lead the parasite to become persistent within the lake, rather than the typical epidemic situation as observed in smaller bodies of water.