The tropical flood plain Pantanal is one of the world’s largest wetlands and a wildlife sanctuary. Mercury (Hg) emissions from some upstream gold mining areas and recent findings of high natural Hg levels in tropical oxisols motivated studies on the Hg cycle in the Pantanal. A survey was made on total Hg in the most consumed piscivorous fish species from rivers and floodplain lakes in the north (Cáceres and Barão de Melgaço) and in the south part of Alto Pantanal (around the confluence of the Cuiabá and Paraguai rivers). Samples were collected in both the rainy and dry seasons (March and August 1998) and included piranha ( Serrasalmus spp.), and catfish ( Pseudoplatystoma coruscans, pintado, and Pseudoplatystoma fasciatum, cachara or surubim). There was only a small spatial variation in Hg concentration of the 185 analyzed fish samples from the 200×200 km large investigation area, and 90% contained total Hg concentration below the safety limit for regular fish consumption (500 ng g −1). Concentration above this limit was found in both Pseudoplatystoma and Serrasalmus samples from the Baı́a Siá Mariana, the only acid soft-water lake included in this study, during both the rainy and dry seasons. Concentration above this limit was also found in fish outside Baı́a Siá Mariana during the dry season, especially in Rio Cuiabá in the region of Barão de Melgaço. The seasonal effect may be connected with decreasing water volumes and changing habitat during the dry season. The results indicate that fertile women should restrict their consumption of piscivorous fishes from the Rio Cuiabá basin during the dry season. Measures should be implanted to avoid a further deterioration of fish Hg levels.