The biodiversity of stream-dwelling fish and the effects of oil palm and acacia plantations on this biodiversity were evaluated by field research conducted in the Bintulu region of central Sarawak, Malaysia. A quantitative survey was conducted at 61 locations by electrofishing. These 61 locations included 16 sites in oil palm plantations, five sites in acacia plantations, four sites in local community-protected forests (called pulau or pulau galau by local communities) and 36 sites in natural forests. The protected forests had the highest species richness (average ± standard deviation: 9.3 ± 2.6) followed by natural forests (7.4 ± 3.1). The species richness of oil palm (3.3 ± 1.9) and acacia (4.0 ± 1.9) plantations was approximately half that of protected and secondary forests. Cluster analysis suggests that the fish fauna was largely divided into two main groups: the plantation group and the forest group. Statistical analysis by a generalised linear model also suggests that plantations have a negative impact on fish diversity as species richness, the number of individuals and Shannon’s diversity index were all negatively affected by both oil palm and acacia plantations. The models included topographical parameters, such as slope and altitude, but the effect of plantations was much stronger than the effects of these parameters, indicating that there was no spurious relationship between plantations and fish communities. In this chapter, we evaluate the negative effect of plantations on fish biodiversity. The mechanisms by which plantations affect fish biodiversity need to be investigated in the future.