Hypereutrophic conditions in lake ecosystems are generally associated with nutrient inputs from surrounding terrestrial landscapes. However, some systems can receive primary nutrient inputs through hydrologic connections such as rivers or canals. Lake Carlton, Florida, USA is a small, shallow, polymictic lake that ends a hydrologically connected string of lacustrine systems with hypereutrophic lakes Beauclair and Apopka. Lake Beauclair and Lake Apopka were connected hydrologically when a system of canals was constructed beginning in 1893 CE. These lakes have maintained hypereutrophic conditions despite extensive management to reduce nutrient inputs. Here, we collected a sediment core from Lake Carlton to accomplish two primary research objectives: 1) reconstruct the nutrient input for Lake Carlton throughout the last ~ 150 years to conduct source assessment, and 2) link primary producer changes with management actions between lakes Apopka, Beauclair, and Carlton. Paleolimnological tools were applied to a 165-cm sediment core and analyzed for bulk density, organic matter content, nutrients (C, N, P), photosynthetic pigments, and total microcystins. Sediments were dated using 210Pb and results indicate that the core represents over 150 years of sediment accumulation. Sedimentary nutrient concentrations show that the primary driver of nutrient inputs resulted from canal construction, beginning in 1893 CE, which corresponded to increased nutrient deposition. Photosynthetic pigment data indicate dramatic increases in most primary producer groups coinciding with the hydrologic modification. However, around ~ 1970 CE, primary producer communities shifted from diatom dominance to cyanobacterial dominance, which appeared to be linked to internal nutrient dynamics and competition among phytoplankters within the lake ecosystem. Cyanotoxin production records show a significant lag between cyanobacterial dominance and peak cyanotoxin production with toxins increasing in the last 30 years. These data demonstrate that local nutrient inputs do not govern all phytoplankton dynamics in shallow lake systems but must be interpreted considering hydrologic alterations and management practices.