To evaluate changes in abundance and composition of phytoplankton in the San Ignacio-Navachiste-Macapule Lagoon Complex in the Gulf of California during the wet-dry transition months, 18 sampling sites were established. Samples were analyzed for abundance, chemical water composition, temperature, and Secchi disk measurements in September, October, and November 1998. The combined effects of rainfall, municipal wastewater, and agricultural drainage yielded runoff that generate low salinity, high concentration of nutrients, low pH, and high biochemical oxygen demand conditions. Temporal and spatial patterns of phytoplankton related to these drainage waters were mapped. The highest concentrations of chlorophyll (15 mg/m3 ), maximum phytoplankton abundance (3.7 × 106 cells/L), and dominance by microphytoplankton (cells > 20 µm) occurred with the high runoff contribution of September. Phytoplankton concentrations (cells/L) decreased in October (1.6 × 106 ) and November (2.3 × 106 ), and the community was dominated by nannoplankton (cells < 20 µm). Cluster analysis showed the influence of runoff in the distribution of species, as well as abundance of cyanobacteria (5.5 × 105 cells/L), higher in the inner lagoon in September and October. The study clearly showed a relationship between the development of phytoplankton blooms and the input of nutrients
