Few studies have examined cyanobacteria persistence starting from lacustrine cyanobacteria harmful algal blooms (HABs) downstream. Multiple lakes and reservoirs within New Jersey's Raritan Basin Water Supply Complex (RBWSC) feature recurrent HABs and discharge water into the Raritan River. As the RBWSC provides drinking water to 1.5 million people, these HABs create drinking water treatment and human health concerns. This study quantitatively reviews the persistence of cyanobacteria communities across the RBWSC from cyanobacteria-dominated lacustrine sources to downstream drinking water and qualitatively assess what, if any, water chemistry parameters influenced the persistence, growth, or decline of cyanobacteria during downstream transport. Statistical tests showed there was a lack of continuity between cyanobacteria communities along the Raritan River, except for periods of higher streamflow and higher releases from the Spruce Run Reservoir. Results along the Millstone River suggested the potential for in-river cyanobacteria growth, which overlapped with periods of low streamflow and high nutrient concentrations in the summer and fall. A permutational analysis of variance (PERMANVOA) test found significantly dissimilar (p < 0.01) cyanobacteria communities between lake and reservoir outlet sites and downstream sites in the Raritan, but not the Millstone River (p = 0.928). A similarity percentage (SIMPER) analysis found cyanobacteria communities changed from high densities of bloom forming cyanobacteria (Aphanocapsa, Aphanizomenon, Microcystis) at the lake outlet sites to low densities of non-bloom forming cyanobacteria (Synechcoccus, Chroococcus) along the Raritan mainstem, with Aphanocapsa the most notable bloom forming genera overlapping between sites. Investigating cyanobacteria on a watershed-specific basis could enhance understanding of the site-specific transport mechanisms and water chemistry parameters that facilitate community persistence.