Although cyanobacteria are commonly associated with eutrophic lakes, they are the basic components of phytoplankton communities in lakes that have different trophic statuses. In inland waters, both nutrient loading from watersheds and warmer conditions promote phytoplankton growth and cause extensive cyanobacterial blooms. Certain bloom-forming cyanobacterial species can pose a health risk to humans and aquatic ecosystems through cyanotoxin production. The aim of this study was to evaluate the cyanobacterial composition and toxins in five reservoirs and two natural lakes in the Kucuk Menderes River Basin, all with varying trophic statuses. Within this scope, samples were collected in autumn 2017 and spring 2018. Cyanobacterial species were enumerated according to the Utermohl method. Cyanotoxin samples were analyzed using HPLC. To find the trophic status of the water bodies, the Trophic State Index (TSI) developed by Carlson (1977) was used and Total Phosphorus (TP), Secchi Depth (SD), and Chlorophyll-a (chl-a) measurements were performed. Cyanobacterial abundance, species composition, and cyanotoxin production differed significantly between the lakes and reservoirs. A total of 13 cyanobacteria species were identified including potential cyanotoxin producers such as Microcystis, Aphanizomenon, and Dolichospermum. According to the TSI, three reservoirs were mesotrophic and the other four waterbodies had eutrophic-hypereutrophic conditions. Microcystis is the most common bloom-forming freshwater cyanobacteria in the Kucuk Menderes River Basin. However, microcystin concentrations were relatively low and the highest microcystin concentration was detected in the Tahtali Reservoir at 9 mu g/L. The Kucuk Menderes River Basin is under water-stressed conditions and the cyanobacteria blooms in the region might pose another threat for wildlife and humans.