The composition and abundance of distinctive planktonic autotrophs (ca 60 taxa) were examined at roughly fortnightly intervals in two sizeable reservoirs (Midmar and Albert Falls) on the uMngeni River, KwaZulu-Natal, between 1989 and 1997. The dynamics of community structure and abundance were examined in both taxonomic and functional (C-S-R) terms in relation to physical abiotic variables (thermal stratification, light climate, water level) and biotic influences of predation (zooplankton abundance). Annual periodicity was exhibited by most taxa apart from Cryptomonas, although patterns tended to be indistinct and inter-annual repeatability was generally weak – in line with year-to-year and between-system environmental variability. Water level fluctuation, with concomitant change in stratification intensity and hydraulic mixing and accompanying changes in water clarity associated with suspended sediment levels was clearly a major (direct and indirect) determinant of phytoplankton composition and abundance. The influence of top-down controls as inferred from phytoplankton-zooplankton relationships was fundamentally different in the two reservoirs – potentially stimulatory in Midmar, but clearly regulatory in Albert Falls, where episodic collapses of Daphnia populations resulted in chlorophyll values well into the eutrophic level range. In addition to annual patterns, changes in chlorophyll content implied progressive long-term changes in trophic status, especially in Albert Falls, with the emergence of various ‘new' taxa (and/or higher peak densities of others). Consideration of phytoplankton dynamics in terms of functional groups offers certain advantages over conventional phyletic taxonomic analyses, although algal response forecasting by either approach appears potentially constrained by hydrological variability. Site-specific bio-monitoring, possibly using new rapid technologies, is likely to be necessary for ongoing management purposes until predictive capabilities under regionally characteristic conditions improve. Despite limitations, functional classification proffers faster advances to this end than conventional taxonomic appraisal. Water SA Vol 32(1)pp:81-92