The abundance and diversity of zooplankton and macro invertebrate communities in the Fogera floodplain was studied in 2010/2011. Three study sites were established in the study area which has the same microhabitats. Physico-chemical data was taken in situ using combined meter for T0, pH, TDS and Conductivity and secchi depth for water transparency. The result of two way ANOVA indicated that all physic-chemical parameters showed significant spatial and temporal variation. Zooplankton and Macro invertebrate samples were also taken at the same time and site as that of the physico-chemical variables using standard mesh sized net. The data was sorted and identified at family level in the laboratory. A total of 26 taxa comprising of 4,344 individuals of macro invertebrates were collected from the study sites. The taxa richness at the study sites ranged from 21 at AM to 24 at TQ and AB while the individuals number ranged from 1233 at AM to 1664 at AB. Invertebrate species richness was dominated by collectors and predators at all sites. Collectors were relatively higher at (AB), while predators were higher in abundance and diversity in all sites. The abundance of macro invertebrates showed seasonal and temporal variation being higher at AB during the wet season. But taxa richness did not show significant spatial and temporal variation. Some of the macro invertebrates metrics calculated from the sample data showed spatial and temporal variation. The metrics SDI, evenness index and percent taxa richness were lower during the dry season while DT was higher. The sensitive metrics (SDI and TR) showed negative correlation with T0, pH, TDS and Conductivity and positive correlation with secchi depth while DT responded in the opposite way. Zooplankton community in the study sites was dominated by copepods in all sites which contributed 88% of the total community and were best represented by calanoids while Cladocerans and rotifers were the least abundant groups. In general the floodplain was dominated by rice farming and has favorable environment for aquatic fauna including fish although the area was threatened by anthropogenic impacts (over grazing and irrigation). Therefore, the wise use of resources should be adapted to maximize effective utilization of these resources by developing environmentally meaning full strategic plans and implement a catchment-based floodplain management and conservation activities to address the upcoming problems.