Our study evaluated spatiotemporal variation of physicochemical parameters and benthic and sestonic algal biomass in littoral areas of the main channel and floodplain lakes of the Cinaruco River, a lowland tributary of the Orinoco River in Venezuela. The Cinaruco is characterized by a highly predictable annual flood pulse, high transparency, and extremely low conductivity and suspended sediment load. During 2002 and 2003, 10 sites in the main channel and floodplain lagoons were sampled on 12 occasions. Correspondence analysis based on water physicochemical variables and algal biomass showed that ˜80% of the variation in the multivariate space among sites and sampling dates was explained by 2 axes. During the high-water periods, river and lagoon sites showed high similarity in water variables and algal biomass. Conductivity, SiO₃, and chlorophyll a concentrations (both benthic and sestonic) were low during the high-water phase. On the other hand, water variables and algal biomass differed between river and lagoon sites during the low-water period. The absence of flow in lagoons and consistently low algal biomass (sestonic and benthic) in river sites were the most important features of the spatial variability between main channel and lagoon sites during low-water phases. Benthic chlorophyll a was highly uniform at small spatial scales and significantly heterogeneous at large spatial scales. The annual flood regime of the Cinaruco, which drives the concentrations of dissolved materials and affects material interchanges between aquatic and terrestrial systems, also appears to be responsible for creating strong patterns of seasonal and spatial variation in benthic algal crops.