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Once every three, four or even seven years, the Southeast trade winds which blow west-ward across the tropical zone of the Pacific Ocean, from the shores of South America towards the Asian land mass, weaken and sometimes even reverse their direction. This phenomenon is known as El Nino. Conversely, the climatic condition known as La Nina is characterised by unusually cold ocean temperatures in the equatorial Pacific, as compared to El Nino. Global climate anomalies associated with La Nina tend to be opposite to those of El Nino. A study of shrimp culture in Ecuador was carried out to analyse the temporal changes in pond water quality, phytoplankton composition and diversity, and bacterial composition and diversity in the intestines of cultured Litopenaeus vannamei in Ecuador. These parameters were studied in relation to their impact on the growth, survival and production in a semi-intensive shrimp culture farm situated in the Chone River Estuary, Ecuador. Five culture periods were studied during the climatic events of El Nino, La Nina and transition periods (1996 to 1999 ). Shrimp were stocked in ponds at 10 PL/m2. Pond management included pond drying, inorganic fertilisation, and feeding with a commercial pellet twice a day. The physicochemical characteristics of the pond water and the phytoplankton and bacterial counts were estimated at intervals of 7-15 days of culture during each period of study. The concentrations of nitrite, nitrate, sulphide, ammonia, pH and suspended solids in the pond water in all ponds during the five culture periods fluctuated within ranges considered compatible with shrimp farming. Phosphorus, silica, temperature and salinity, however, showed significant differences during the five periods of shrimp culture, reaching sub-optimal levels during some culture periods. The species composition and diversity of phytoplankton was different during El Nino, La Nina events and transition periods, with a decrease in the diatom community and an increase in the cyanophytes algae community associated with changes in nutrients and nutrient ratios, and temperature, salinity is discussed. A low diversity of bacterial genera with a predominance of Vibrio spp., particularly V. harveyi and V. parahaemolyticus, was observed in shrimp intestines during disease outbreaks in the transition and La Nina periods associated with significant environmental changes in temperature and salinity. Shrimp performance was significantly different between El Nino, La Nina and transition climatic periods. Survival, feed conversion ratio and yield were better during El Nino periods because of the positive effects of higher pond water temperature and salinity (29°C and 28 psu) on the shrimp stocks.