Ibuprofen (IBP) has demonstrated its toxicological potential toward aquatic biota: affecting microalgae and their nutritional value and altering the population growth of algae-feeding zooplankters. This study assessed the effect of a) IBP sublethal concentrations, and b) three different algal densities (Nannochloropsis oculata at 0.25, 0.50, and 1.00 × 106 cells/mL) on Alona guttata and Lecane papuana. We determined LC50 values for both species (63.476 mg/L and 12.053 mg/L, respectively), and then five sublethal concentrations (based on their respective LC50) were chosen to assess population growth effects. Survival and fertility of A. guttata were affected at the two highest concentrations tested, diminishing population growth, but seemed non-affected by the algal density. In contrast, L. papuana was significantly affected by both factors, IBP and algal concentrations, showing higher sensitivity to IBP at the lowest algal density (EC50 = 0.524 mg/L) in comparison to those organisms fed on 1 × 106 cells/mL (EC50 = 3.097 mg/L). Discussion considered the availability of energy in terms of algal density, the possible biomagnification of IBP from algae to zooplankters, and the algae-mediated biotransformation and removal of IBP. Thus, the interactions of these factors could have mediated the differential effects observed between A. guttata and L. papuana.