This study addresses the gap in understanding the diversity, species, and functional trait distribution of different algal groups that occur in the Okavango Delta (a near-pristine subtropical wetland in northwestern Botswana) across hydrological and habitat gradients. We systematically characterize the delta’s algal flora, addressing the gap left by previous research that was limited to single algal groups (e.g., diatoms) and/or only looking at upstream areas in the Okavango River basin. We analyzed 130 algal samples from 49 upstream and downstream sites with higher and lower flooding frequency, respectively, across a river-to-floodplain habitat gradient. Chlorophyta and Bacillariophyta dominated both abundance and taxon richness (>80%) of the total 494 taxa found from 49,158 algal units counted (cells, colonies, coenobia, and filaments). Smaller algae were more abundant in downstream floodplains than in upstream channels and lagoons. Motile and siliceous algae were much more abundant than non-motile, nitrogen fixing, and phagotrophic algae. The frequency of these traits was associated more with flooding frequency than habitat type. The highest algal richness and diversity were found downstream, where shallow floodplain ecosystems with seasonally fluctuating water depths offer greater habitat heterogeneity, and macronutrients are resuspended. The increasing threats from upstream water abstraction plans, fracking, and climate change require enhanced protection and monitoring of the Okavango Delta’s natural annual flood-pulse to maintain the high species and functional diversity of this unique wetland’s microalgae.