Synthetic non-metallic nanoparticles (NMNPs) such as carbon nanotubes (CNTs), carbon nanodots (CNDs), and cell-penetrating peptides (CPPs) have been explored to treat harmful algal blooms. However, their strain-specific algicidal activities have been rarely investigated. Here we determined their acute toxicity to nine freshwater cyanobacterial strains belonging to seven genera, including UTEX 2386, UTEX 2385, LE3, PCC 7122, sp. NZ, SB 1810, sp. PCC 6803, sp. CCAP 1446/10, and CAWBG635 ATX. We prepared in-house three batches of CNDs using glucose (CND-G) or chloroform and methanol (CND-C/M) as the substrate and one batch of single-walled CNTs (SWCNTs). We also ordered a commercially synthesized CPP called γ-Zein-CADY. The axenic laboratory culture of each cyanobacterial strain was exposed to an NMNP at two dosage levels (high and low, with high = 2 × low) for 48 h, followed by measurement of five endpoints. The endpoints were optical density (OD) at 680 nm (OD) for chlorophyll-a estimation, OD at 750 nm (OD) for cell density, instantaneous pigment fluorescence emission (FE) after being excited with 450 nm blue light (FE) for chlorophyll-a or 620 nm red light (FE) for phycocyanin, and quantum yield (QY) for photosynthesis efficiency of photosystem II. The results indicate that the acute toxicity was strain-, NMNP type-, dosage-, and endpoint-dependent. The two benthic strains and sp. were more resistant to NMNP treatment than the other seven free-floating strains. SWCNTs and fraction A14 of CND-G were more toxic than CND-G and CND-C/M. The CPP was the least toxic. The high dose generally caused more severe impairment than the low dose. OD and OD were more sensitive than FE and FE. QY was the least sensitive endpoint. The strain dependence of toxicity suggested the potential application of these NMNPs as a target-specific tool for mitigating harmful cyanobacterial blooms.