This study determines the relationships between water flow and water quality in three types of channels in southern Florida, USA: Shark River Slough, Peace River, and Hillsboro Canal. Peace River most resembles a natural channel with floodplain connectivity, sinuosity, and uninhibited flow. Shark River Slough has a natural, shallow channel with sheet flow, while the Hillsboro Canal is the most modified channel due to dredging, straightening, and regulated flow. Hydrologic indices for each channel were estimated to characterize flow regimes and flow variability, while concentration–discharge (C–Q) relationships were determined to quantify the impact of flow regime on water quality. The greatest variability in flow occurred at the Hillsboro Canal, followed by Peace River and Shark River Slough. Connectivity to floodplains and long durations of low and high flow pulses at Peace River and Shark River Slough contributed to the dilution of water quality constituent concentrations at higher flows. Conversely, the channelized characteristics of the Hillsboro Canal resulted in an enrichment of constituents, especially during high flows. This study suggests that C–Q relationships can be used in canal discharge management to prevent water quality degradation of sensitive downstream wetland and aquatic ecosystems.