Intracellular benthic microcystins and microcystins dissolved in water were detected in seven reservoirs in the Segura and Jucar basins located in a semiarid area in the province of Alicante (SE, Spain). Three varieties of intracellular benthic microcystins were identified: Mc-LR, Mc-RR and Mc-YR. Generally, all the microcystin varieties were present in the same reservoir and Mc-LR, considered the most powerful carcinogen known, predominated in most of them. Total microcystins absolute values per dry weight varied from 0.055 μg g−1 in the Elx reservoir in summer to 1.032 μg g−1 in the Crevillent reservoir in spring. Microcystins dissolved in water were not frequent in the reservoirs and were detected in Guadalest throughout the year, with values of between 0.041 and 0.069 ppb. In the Crevillent reservoir, dissolved microcystins were recorded only in summer with 0.163 ppb and were not recorded in the other reservoirs in any season. The cyanobacterial presence varied throughout the year, but no significant difference was seen for interseasonal microcystins production (ANOVA, p > 0.1). The principal component analysis (PCA) and Pearson's correlation coefficient results showed that physico-chemical parameters did not significantly account for both intracellular and dissolved microcystins occurrence. Moreover, the PCA indicated that the evolution of the concentrations of dissolved and intracellular microcystins followed different patterns. The fact that benthic organisms could release intracellular toxins into water may be due to stress caused by changes in water levels and by colonies’ senescence. However, they may also perform antigrazing and/or allelopatic functions. A significant difference was found for conductivity, phosphates and the presence of microcystins Mc-LR and Mc-Tot in the oligo- and eutrophic reservoirs (t test, p 0.1). In fact, microcystins were never detected in the more eutrophic reservoirs, e.g. Tibi and Beniarres, both of which correspond to the River Jucar basin. This fact indicates a significant difference for conductivity and the presence of microcystins Mc-RR (t test, p < 0.1) between the River Segura basin and that of the River Jucar. The identification of microcystins in benthic cyanobacteria from the less eutrophic semiarid studied reservoirs showed that hepatotoxin production was restricted to neither planktonic species nor the physico-chemical parameters considered typical for the occurrence of cyanobacterial toxins.