Microcystin (MC) risk is often assessed within bloom-affected lakes and reservoirs, although hydrological connectivity can extend exposure into downstream river and estuarine networks. We synthesize evidence using a lake–river continuum framework that treats connected reaches as active processing environments. The framework separates the source pool, export flux, and downstream exposure, and distinguishes advective redistribution, reversible retention, irreversible transformation, and source or remobilization processes. Hydrology sets reaction opportunity, while phase partitioning, photochemical and microbial transformation, sediment exchange, and biological uptake determine how MC mass and bioavailability change during transport. Field evidence shows that downstream occurrence cannot be inferred reliably from visible source blooms: reaches may attenuate, retain, redistribute, or locally renew MC exposure depending on hydraulic state and process coupling. These dynamics shift exposure among water, particles, sediments, cells, and biota. Consequently, source-lake indicators or water concentrations alone can mischaracterize ecological exposure, and drinking-water guideline values are not ecological protection thresholds. Key priorities are flux-resolved monitoring, direct field estimates of process rates and transformation products, chronic ecotoxicology matched to realistic exposure routes, and hierarchical transport–biogeochemical models. This continuum perspective links source, process, pathway, receptor, and effect within a single source-to-risk framework.