The deeper, warmer water in the east limits the amount of nutrient-rich deep water normally surfaced by the upwelling process. Since fish can no longer access this rich food source, many of them die off. This is why these conditions are called "El Nino", or "the Christ Child", which is what Peruvian fisherman, calls the particularly bad fishing period around December. More importantly, the different water temperatures tend to change the weather of the region.
What happens to the ocean also affects the atmosphere. Tropical thunderstorms are fueled by hot, humid air over the oceans. The hotter the air, the stronger and bigger the thunderstorms. As the Pacific's warmest water spreads eastward, the biggest thunderstorms move with it. If you look on a map, you will see that suddenly islands like Tahiti, normally tropical paradises, experience massive storms.
The clouds and rainstorms associated with warm ocean waters also shift toward the east. Thus, rains which normally would fall over the tropical rain forests of Indonesia start falling over the deserts of Peru, causing forest fires and drought in the western Pacific and flooding in South America. Moreover the Earth's atmosphere responds to the heating of El-Nino by producing patterns of high and low pressure which can have a profound impact on weather far away from the equatorial Pacific. For instance, higher temperatures in western Canada and the upper plains of the United States, colder temperatures in the southern United States. The east coast of southern Africa often experiences drought during El Nino (NASA Science Content Manager, ea.al, 2003).