Freshwater zoobenthos (macro-invertebrates) are organisms that live on, in, or near the bottoms of the freshwater. Their presence, abundance and species diversity are affected by numerous factors. This study was designed to evaluate temporal and spatial changes of benthic invertebrates' diversity in the light of ecological conditions at the selected sites. Three sites at Menoufia governorate were selected as follows: site one and two are located at Bahr Shebeen El-Koom, Milig and Tanta branches, respectively. However, site three is located at Gezay Village, Menouf. Monthly samples were collected during one year from March, 2017 till February, 2018. Ecological parameters such as temperature, pH, total dissolved solids (TDS), electrical conductivity (EC)…etc., and heavy metals (Al, Ca, Cu, Fe and Pb) concentrations in sediment and tissues of the collected molluscs were measured. Environmental parameters showed variations in values from one season to another. The highest abundance of zoobenthos in all seasons was recorded at site three (42 %) followed by site one (32 %) and then site two (26 %). Three phyla were recorded during the present study; Annelida, Arthropoda and Mollusca. Diversity, variety and evenness indiceswere maximum at site three followed by site one then site two. Heavy metals concentrations in sediments and tissues of mlousca were maximum at site two followed by site one and finally site three. It is concluded that, the population density, species diversity and communities of freshwater benthic invertebrates were fluctuated in numbers and distribution mostly under the effect of the habitat they live in (spatially) than under the effect of season (temporally) in the present investigation.