Within New Jersey’s Raritan Basin Water Supply Complex, multiple lakes and reservoirs with persistent and recurrent cyanobacterial harmful algal blooms (cyanoHABs) discharge water which ultimately travels downstream in surface water to drinking-water intakes. Cyanobacteria and other water-quality data were collected as part of a collaborative study among multiple agencies, including the U.S. Geological Survey (USGS) New Jersey Water Science Center (NJWSC), New Jersey Water Supply Authority, New Jersey Department of Environmental Protection, and Montclair State University to evaluate the spatial and temporal variability of cyanotoxin occurrence and potential production, persistence, and transport from lacustrine sources to downstream fluvial systems used as a drinking-water source in the Raritan Basin Water Supply Complex, New Jersey. An advanced monitoring strategy using a combination of solid phase adsorption toxin tracking (SPATT) passive samplers, discrete water-quality samples, and continuous monitoring instrumentation, were used to help gain insight on rapidly changing water-quality conditions that affect cyanotoxin production and transport. Eight discrete sampling locations were chosen based upon existing USGS streamflow-gaging stations as well as one site located on Spruce Run Reservoir. Twenty discrete sampling events were conducted across the 8 river sampling locations and 24 sampling events from the reservoir sampling location from August 2020 through August 2021; events occurred twice per month except from December 2020 to April 2021, when samples were collected once per month. Each sampling event was spread over two days, with upstream sites sampled on the first day and downstream sites sampled on the second day. This sampling method mimicked the natural order of streamflow. To meet study objectives, certain types of data were collected, including streamflow, discrete water quality and turbidity samples, water-quality field measurements (water temperature, pH, dissolved oxygen, and specific conductance), nutrients (ammonia, orthophosphate, nitrate plus nitrite, total phosphorus, and total nitrogen), chlorophyll-a, cyanobacterial genes (cyanobacteria 16S cyanobacterial ribosomal RNA, and cyanotoxin synthetase genes for microcystin, saxitoxin, anatoxin-a, and cylindrospermopsin), cyanotoxins (microcystin, anatoxin-a, and cylindrospermopsin), and phytoplankton.