1. Climate change affects aquatic ecosystems differently depending on local conditions. In the Mediterranean region, predicted drier seasons could especially affect lake water residence time and in consequence cyanobacteria and cyanotoxin dynamics.
2. We carried out a 3-year study of a shallow, Mediterranean lake (Lake Albufera, Spain), to study the effects of water residence time and other drivers on the dynamics of harmful cyanobacteria and microcystin concentrations (MCYST).
3. Longer water residence time in dry years and dry seasons increased total cyanobacteria biomass, Microcystis aeruginosa populations and MCYST concentrations in the lake water and seston. Droughts increased water retention time by about 45%, and M. aeruginosa populations and MCYST were 1–2 orders of magnitude higher.
4. All samples analysed contained MCYST, and among them 70% had values above the recommended guidelines. Flows lower than 10 m3 s−1 raised toxicological risk from low to moderate-high according to international standards. Mean MCYST concentrations bound in the cells were one order of magnitude higher than in the water (11 ± 2.9 and 1.2 ± 0.3 μg L−1, respectively).
5. The microcystin content per unit biovolume of M. aeruginosa was generally higher at the start of population growth (April–May) than at the population maximum (July–October). This was related to increase in water residence time, total phosphorus concentration and mean colony size within the edible range (<50 μm). The maximum MCYST content corresponded with average populations of 103 colonies L−1 and 2 mm3 L−1, which could additionally be used to evaluate toxicological risks in the lake.
6. Microcystis aeruginosa colonies were larger with increasing water residence time and more closely related to the lake hydrology and water column stagnation than to MCYST colony content.
7. Feasible measures for restoration and conservation of shallow Mediterranean lakes in a future climate scenario are discussed.