We discuss the distribution and native status of 24 minnow species (family: Cyprinidae) collected at 203 randomly selected lakes in the northeastern USA (New England, New York, New Jersey) by the Environmental Monitoring and Assessment Program (EMAP). Twenty-four species were collected during the summers of 1991–96. Only golden shiner was frequently collected, occurring in 71\% of the sampled lakes. Fallfish, creek chub, and common shiner were also common. The remaining species were taken in \<10\% of the lakes. Physical (surface area, depth, elevation), chemical (pH, total phosphorus), and watershed disturbance characteristics of the lakes show distinct species-specific patterns. Evidence suggests that native minnow biodiversity has declined over the last 150 years as a result of changing biotic, physical, chemical, and watershed characteristics.