The study identified zooplankton biotypes of the increasingly in-stream sand-mined Imo River in Etche, a Delta area of Nigeria, as indicators of the health of the aquatic ecosystem. Plankton samples were collected with a 55µm mesh size plankton net that was hauled horizontally along the river course for 5 minutes at 7 sampling locations once monthly for 24 months (March 2007-February 2009. Samples were fixed/preserved in 4% formalin solution in labelled plastic containers. In the laboratory, a wide-mouthed pipette was used to withdraw 1ml of the plankton subsample and to place it on a Sedge-wick rafter-counting chamber. Standard keys were used for species identifications and counts made through direct microscopy. The ANOVA, post-hoc plots of group means, hierarchical cluster analysis (HCA), and the Margalef's species diversity index were used to analyze data. Zooplankton had low diversity index (0.926 ± 0.100) and was made up of 7 taxa and a mean density of 433 organisms/ml; with order of dominance as Cladocera (25.87%)> Copepoda (20.55%)> Protozoans (19.17%)> Rotifera (18.71%)> fish eggs and larvae (9.24%)> Crab larvae (4.62%)> Beetle larvae (0.69%). Plankton abundance peaked in sampling location 1 (140 organisms/ml; 32.41%) and was least in location 3 (21 organisms/ml; 4.86%), even as there was marked spatial heterogeneity in the taxa composition [F (11.94) >F crit(3.94) ] at P<0.05. The HCA revealed that crab larvae, fish eggs and larvae, beetle larvae, and copepods formed the first and richest cluster, while the rotifers, cladocerans and protozoans formed the sparse 2 nd , 3 rd and 4 th clusters, respectively. The low biotic diversity recorded could be attributed to growth-limiting perturbations created by ongoing in-stream sand mining in water columns.