Huayuan River and Dong River are two important freshwater rivers, in western Hunan, and strongly affected by Mn and Pb-Zn mining and processing activities. The assessment for potential ecotoxicity risk of surface sediments of two rivers had never been conducted in a comprehensive way. The surface sediments were sampled and total contents of 7 heavy metals including Cd, Pb, Cu, Ni, Cr, Zn, and Mn were measured. The geo-chemical fractions of heavy metals were determined by BCR sequential extraction procedure. The pollution characteristics of heavy metals were evaluated according to Nemerow index and geo-accumulation index, and pollution sources were discussed. The heavy metal ecotoxicity risks were assessed with the application of Sediment Quality Guideline (SQG) (threshold effect level/probable effect level, TEL/PEL) and toxic units approach. The results showed that the total contents of Cd, Pb, Cu, Ni, Cr, Zn, and Mn in the surface sediments from most sampling sites of two rivers were greatly higher than that of the reference site, and thus constituted serious combined pollutions. The heavy metal pollution of surface sediments in Huayuan River was clearly heavier than that in Dong River. In Huayuan River, no clear pollution trend was found, the maximal levels of Cd, Pb, and Zn occurred at S6 site, the maximal levels of Cu, Ni, Cr, and Mn occurred at S4 site, and the degree of heavy metal pollution at different sites indicated by Nemerow index was S6 > S4 > S2 > S7 >S3 > S5 >S1. In Dong River, the relatively low heavy metal levels existed in the upstream and the high levels existed in the middle/downstream, the maximal levels of Cd, Pb, Cu, Ni, Cr, and Zn occurred at L6 site, the maximal levels of Mn occurred at L5 site, and the degree of heavy metal pollution at different sites was L4 > L5 > L3 > L1 > L2. In two rivers, the heavy metals with top accumulation were Cd, Pb, Zn, and Mn. The heavy metal levels at different sites were related to the distributions of mining or processing factories, and thus heavy metal pollution might mainly originate from point discharge of mining dregs and mining wastewaters. In most of the sampling sites of Huayuan River, Cd, Pb, and Mn showed a similar geo-chemical fraction characteristic, that is, those bioavailable fractions were greatly higher than the residual fraction, moreover, the percentages of the exchangeable and weak acid soluble fraction of Mn and Cd were much higher than other heavy metals, however, the percentages of the exchangeable and weak acid soluble fraction of Cu and Cr were relatively low. The levels of Cd, Pb, and Zn in Huayuan River surface sediments were greatly above PEL, and the levels of Cd, Pb, Ni, and Zn in the middle/downstream of Dong River were also above PEL, these heavy metals might show a high potential biological toxicity. In Huayuan River, except for S1 site, the surface sediments from other sampling sites showed clear acute toxicity, and the surface sediments from middle/downstream of Dong River also showed clear acute toxicity, therefore, these river stretches should be controlled with great efforts.