Tailings from bauxite mining in Porto Trombetas (Pará state, Central Amazonia, Brazil) was discharged (1979–1989) into Batata Lake affecting about 30% of its area. The lake belongs to a clear-water flood-plain system along the Trombetas River, a tributary of the Amazon River. Siltation is the main perceived factor impacting aquatic and flooded communities. Besides natural regeneration, a program to restore a section of igapó forest in the impacted area (IA) has been conducted since 1991. Decreased light is the main factor reducing total phytoplankton biomass (PhyBM) in IA. We hypothesized that PhyBM in IA increases over time because of the improvement of the underwater light conditions due to the natural regeneration and restoration. We sampled quarterly PhyBM and limnological variables (depth, transparency, temperature, pH, conductivity, dissolved oxygen, turbidity, suspended solids, total Kjeldahl nitrogen, and total phosphorus), over 15 years (2005–2019) at eight sampling sites in the two areas (N = 349). We also obtained daily climatic and hydrologic data. PhyBM was higher in NIA than in IA. The temporal trend in the annual mean of PhyBM increased significantly over time only in the IA, approximating the NIA values, confirming our general hypothesis. The increase of PhyBM in the IA was negatively related to the residual light attenuation caused by non-phytoplankton turbidity and to total phosphorus, and positively to air temperature and site depth (p < 0.05; Marginal r2 = 0.18; Conditional r2 = 0.29). Instead, in NIA, PhyBM was explained only by the increase in air temperature (p < 0.05; Marginal r2 = 0.15; Conditional r2 = 0.34). We concluded that the PhyBM in the IA positively responds to the synergy between increasing light availability, air temperature, and site depth, and decreasing total phosphorus concentrations, regardless of hydrologic phase.